depends what paint & type of panel line you are using.

if you use gundam marker, water type (thicker tip) works better on painted acrylic easier to rub off, oil type marker (thinnest tip) cannot be wiped off and you will clog your marker very fast.

if you using enamel wash (diluted black enamel paint), then you need to use lacquer paint, then a gloss coat to make the surface slippery so you can easily drop the enamel paint it will flow into the seam lines and wait a while let it dry up a bit you can easily wipe off the excess. once fully dried you can spray a top coat of your choice. the gloss coat helps the panel line flow and makes it easier to wipe off the excess.

most people probably have acrylic based paints so enamel wash is not an option. best bet is paint a thicker coat of paint and use a marker (or super fine mechanical pencil if you don't mind grey lines) or a HD 7B or 8B pencil, and be ultra careful when doing the lining, with thicker paint, you can scrap off the panel line excess with a pen knife (carefully & gently). with pencil it's difficult to keep it clean unless you wear a glove and do not touch finished panel line until you top coat them.

a final top coat should always be done after you finished everything.

also if you spray parts by parts, make sure the paint are not too thick if not will affect your fittings.