How do you think about the current bass sounding?

If not sure and want to try new position, maybe you can try re-position your satellite speaker first as lower mid range can possible affect the way you perceive the subwoofer bass.

Make both satellites height identical and the bottom of the tweeter is around your ear level, if you can't do that maybe you can use door stopper to angle it up.

As for subwoofer positioning, maybe you can try pull out the table and leave the sub at the same position so you got your sub around the same distance to your satellite speakers. Try it back and forth see which gives a fuller sounding to you.

Hope that helps 

get yourself a better soundcard like T-Muso for the extra bass boost option 

Why not try move it out from the pc table. Actually sub is low frequency, not much effect in placement unlike high frequency speaker

Speaker should face the longer side of the room, not the current way round. Only 'boomy' speaker can give quantity bass in that configuration, or if the room's enviroment allows it.

Since your room is pretty empty judging from pict, there is nothing to soak up higher frequencies or reverb the lower frequencies. Since room is not treated try not to position subwoofer dead centered between 2 side walls, unless your listening position is 1/3 distance to the far end or listening at the far end of room.

Best position for sub is at the corner of the room IMO. Best if you can move the whole table & set to the windowed corner, speakers facing bed for near field listening. For more bass coverage, set it at the current bed position facing the WC door, that way the bass port is facing a longer side-wall. If the room is squarish / square / alot of indents (current place other table is placed), there will be alot of 'crosspoints' where there will be almost no bass / mids. C3 doesnt have a dominating bass, pretty challenging if you need for more bass, eq can help as te woofer doesnt bottom out easily. good luck!

Some laptops have slightly weak outputs from their integrated audio system. Both PCI soundcard and external USB DACs are essentially the same thing, just packaged differently. I don't think PCI sound cards can fit inside a laptop, thus a more logical choice would be an external USB DAC. You may want to try putting that subwoofer in a down-firing position with the woofer facing the floor (reflecting the bass directly off the floor) and see. Make sure there is a substantial air gap between the woofer and the floor...

Kinda dfficult to find/see any S2000 around the shops, plus pretty pricey too (one of the most expensive models from Edifier). And which "SuperM" is that? Is it the small Bluetooth thingy? If it is then that is worlds apart when compared to the S2000 (including the price also)....

if you liked bass then the Altec will win no matter how it sounds as R1280T isn't bassy in computer speaker range

but since R1280T doesn't have the generic bass of average computer speaker, it won't have bass mudding it's sound

but lets say I were to switch off the VS4621 subwoofer and only compared the two stereo speakers,

The R1280T is extremely full sounding with body and texture compared to the dead plastic sound of VS4621 down firing midranges