Firstly, you need to know that topcoat & compound are totally 2 different things.
topcoat is clear colourless paint to cover and protect anything beneath it.
compound is for polishing, basically an extremely fine sandpaper, to make the surface you are polishing to be very shiny.

topcoat can't remove nub marks, since it's only a layer of clear paint over it, you still can see it.
as for compound, you need to use file, then fine sandpaper, lastly only compound, in this order, then you will get a smooth finish.

I never sanded clear parts before so I can't be sure, but I do think that with compound polishing it's possible
for metallic parts, you clean the nub marks as usual, but NO sanding. Then you touch up using metallic colour markers or paints.

You can sample photos in this thread
http://forum.lowyat.net/topic/488910

As to restore clear parts transparency you can refer here:
http://www.kenzbuilds.com/intermediate.php...ed_clear_parts#

For the metallic parts one the ways i know is remove the nubs with a sharp hobby knife, paint the nubs area with silver and then use clear color over it that the same color as the part. Like if the part was red, use a clear red paint over the silver.

you can still spray paint part by part, it's like airbrush except that you are using spraycans 
use these to hold the parts when spraying them


then poke them into a foam to let the paint dry

Some hobby shop have sold this in sets, you can make yourself with a stick and alligator clip or paper clip from hardware / art stores.

For me i spray facing the windows so the fumes will come out as you spray in a box with a fan at the back to suck fumes out. Unless you get close with the wall with an airbrush it won't hit it as paint will evaporate over distance for normal spray cans is possible since it range is much more larger. 

You can refer to tytroum to get a set in the lyn street mart sale section.

Marker is much more time consuming as it not easy to get a nice finish on large parts without going painting the part multiple times to avoid the brush strokes.

find mooncake81 or tytroum, they do sell this in set.
otherwise buy the alligator clips or book clips and satay stick separately then make yourself.

as for where to spray, you have few options:
- get a painting booth. Expensive but effective and safe.
- build your own painting booth. Get a large box, cut a hole at the back, then put a PC fan or similar small fan for outward suction. Cheaper than buying a painting booth, but you need to work on it.
- spray outdoors. Easiest solution, but might be harmful, and make sure to spray following the direction of the wind or the wind will blow the paint towards you
No, painting with markers actually consume more time, as markers' paint don't give consistent finish. You'll definitely need multiple layers of paint with the marker, while waiting each layer to dry completely(few hours to be safe) before painting the next layer
yes of course the paint will be scratched, and even with 2000 grit sandpaper you still risk scraping off the paint entirely.
only using polishing compound is safe, but the purpose of using that is to polish smooth your paint surface, not to remove nub marks.

and even though you can remove nub marks safely without damaging the paint, you'll still need to paint the areas with nub mark again, which costs you time.
which in the end you'll end up faster if you paint after removing the parts.

as for topcoat, I think the concern here is not whether the scratches on the paint can be covered or not, but whether you get a consistent finish of your paint or not

I will highly against spraying the parts on the runner since it just unnecessary do the job twice as sanding will remove the paint and if you try to paint the part that you remove nub marks will create unevenness to the previous painted surface.

As Nic already said it only protect the surface underneath it, so if it damaged to begin with it will stay damage since top coat is not for fixing the surface unless it a minor scratch which only made them less visible.

reducing the duration of spraying doesn't reduce the toxicity you are exposed to
the best solution is to get a painting booth & a proper painting mask

thanks for the suggesiton...
yeah. basic rules of good finishing is always to have many thin layers..
could anchor be the best ?

another question, altho its a bit obvious...
some painted models i see have kinda shiny inner frames..
are those normal paint with gloss finish?
it really looks like its made of metal/steel..

RM100+ can get a Airbrush hand piece(the gun) but china brand type.
If you're in PJ then you can go to ICW to use their compressor(For free).  A decent compressor would cost at least RM400...
To achieve metalic/metal feel, using air brush is the way to go because hand paint is unable to achieve the smoothness of the paint.
Although spray can have them but they might hurt your plastic OR over spray resulting thick layers
would not recommend this. You will still miss certain parts of the are that you need to spray.
Satay sticks are the way to go. Satay sticks aren't expensive. Get aligator clips or use blu-tac with them to hold your gundam parts.

the reason why i don't recommend that method is because yes once you paint one side then you can flip the parts BUT there is the a risk where when you flip, the painted part's paint might come off due to the double side tape if you're careful.
The best is spray one by one rather than all at once. Yes, you can spray multiple parts depending on the parts then you can spray 2-3 together. 

Because you use tapes so there is a risk of it peeling the paints. Unless you use masking tapes(tamiya) but able to hold small parts.
No matter what before spraying colors, always top coat.

I don't mind giving you guys fundamental tips/skill at icw if you guys meet up together. I can share my knowledge one shot.

Because you use tapes so there is a risk of it peeling the paints. Unless you use masking tapes(tamiya) but able to hold small parts.
No matter what before spraying colors, always top coat.

I don't mind giving you guys fundamental tips/skill at icw if you guys meet up together. I can share my knowledge one shot.

I seldom go on weekends. You adjust the time with me tru pm
Too bad.
Top coat is usually the last step or before you do decaling(optional)

oh sorry for the confusion..
what i meant was before you paint, must PRIME.   
yes.. always prime first.

Here's a very useful Link

If you going to use the same paint on same part, you can skip priming it but do sand it so the paint will have better adhesion on the plastic. If you don't want paint it at all, it is unnecessary to prime it. But prime it is always a better choice, so the color texture will be smooth and properly adhere to the plastic. 

i think you totally misunderstood.
Reason why we prime it is because..
Every part we'll sand it. Why? because once you cut them our from the runners, they will have nib marks. We sand to get rid of the nib marks.
But once we sand, we leave light/heavy scratches on the parts therefore we need to prime.
Prime/surfacer's purpose is to cover the scratches(not the heavy ones) and also make the paint stick "better".
so for us modelers, we prime every single parts except transparent parts because we want to paint it.

Why not paint the white part when already planned to paint other parts.
Top coat does not help cover scratches. It only helps protect the paints and give a nice finishing.

I understand as this hobby requires $$ when starting up.

You're not suppose to use white primer as white paint but if you can live with it then it's up to you.    White primer finishing is not the same as white paints.

i am assuming you're gonna use everything spray cans to spray your kit therefore the $$ load. I've been there before.
Think about it, I used spray  cans to sprayed my MG strike freedom. The kit cost me RM179(few years back) and the spray cans alone already cost me RM200+(mr hobby + tamiya). So it was not worth it unless you use industrial spray cans like others mentioned.

Think about it thoroughly, if you think you are gonna be serious in this hobby why not save the money and get an air brush set like i did. The starting cost might be "painful" but long term wise, it's a good investment. It may take you 400-600(basic set) of air brush but paints cost you like RM8-10 per bottle. 1 White bottle can spray 2-3 MGs.

I hope my long post doesn't bore you and able to help you. I know a guy in Sarawak or Sabah brings in gunpla tools and stuff so at least you won't have to worry about shipping cost so much.

One question, why do you need compound? do you know what it's purpose?