A couple ?s

Pre-shading only works if you don't paint it all out. The idea is to give depth to panel lines. Many people (myself included) just use a sludge wash after the painting is done for the same effect without all the work.

Clear coats come in two basic kinds: glossy and flat. There are more variations than that (semi-gloss, satin, etc.) but those are the main two. Typically you gloss clear coat a flat paint job so decals won't silver (air gets under the decal as flat paint isn't actually FLAT), then once the decals are snugged down another clear coat, this time flat, brings it back to the "proper" finish.

When you apply the top coat after pre-shading, the idea is to not cover the shading completely so it shows through. You achieve this by applying thin layers of paint until you get the desired effect.

Clear coats come in flat or gloss - it really depends why you're applying a clear coat in the first place. Some people apply a clear gloss coat to apply washes and then apply a flat coat afterwards.

can i spray a clear coat over flat colors or will it make the flat colors look glossy?

Yes, If you spray a gloss coat over your flat finish the final finish will appear glossy. If you made a mistake and applied a high gloss coat that wasnt needed you can simply spray a flat gloss coat over this and your finish will return to flat.