Working at higher resolution is not always the best.
Ideally, if a skin is done at 1024x1024, then the best way to skin it is at 1024x1024 and none other.
The largest problem when doing a skin at higher resolutions than it is supposed to be, is that when it is reduced in size, no matter how good the graphics program is, you will experience a sharp drop in quality.
This is especially problematic when, for example, you try to make emblems, markings, or numbers in higher resolution/larger size than it is supposed be. A Hakenkreuz(the german cross) done twice the size as it is supposed to be might look great, but if you reduce it in size to match the actual size that would be applied to the wings, then you will get ugly anti-aliased borders - fuzzy and unclear.
My recommendation is, if you are creating markings, emblems, panel lines, dots, rivets and anything that needs a very clear depiction, do it in the original size/resolution.