Question(s)

[major_setback]

These are better templates, even if they also aren't multi-layered (they are also official).
http://airwarfare.com/sow/index.php/...-cod-templates
Try some of the user made templates at the site too. They are multi-layered.

Rivets and panel lines you can't change.

Some skins have default warnings and stencils (ex. Hurricane, Bf 109) though it varies a lot between aircraft, and some have very little. I added lots of stencils and warning markings to my Heinkel 111s at that site. You can can usually find some extra things to add to an aircrat if you want.

I'm not sure what you mean about markings. You can turn them off in-game for your aircraft, (or for any other aircraft using Full Mission Buider and un-ticking the appropriate box). So any sking you make can have it's own roundel if you have added it during the making of your skin.
You can't make custom roundels of your own and have them automatically applied to aircraft.

[Edit: The templates I linked to above seem to be a combination of the default weathered layer, and rivet/panel line layer. They originally came from the Cliffs of Dover french forum, but they have definately been made by someone with access to these two layers]

Cheers. Setback