I started out messing with PC graphic proggies back when all there was was Dos, but eventually graduated to Windows OS where the weapon of choice for me was always PSP [Paintshop Pro].

I'm still mostly using PSP [now '6'] and over those decades I've almost always worked with 'flat' graphics [single 'layer'].  Sometimes I'll add another raster layer, throw on some graphics and use the trans option to 'blend' into the background [primary graphic], but still ultimately merge them to save as BMP.

It really is a silly way to work but the short-comings of the method pushes you to find work-arounds - other manipulation 'skills'...one of my faves is the 'push' brush.

Maybe it's all just therapeutic to do it 'the hard way', or I'm just a sucker for punishment.

Lately I've dragged out my PS ver [Elements 2] and have been messing with the PSDs that sometimes come with some of the addon aircraft for FSX [MS Flight Sim 10].  The 'mechanics' of it is a bit of a pain [not yet intuitive] but quite a bit of 'fun' all the same.

The 'issue' with flat raster work is that often you end up working on a per pixel level.....literally painting them one at a time.

It's that sort of pain/detail/effort that can expose the short-comings of image generator software - where the latter paints with such a 'broad brush' that they often fall down on close scrutiny.

My graphic background was a long time pre the computer age where there were no real shortcuts other than to draw by 'suggestion' or even omission.... where what you leave out is just as important as what you include.

So much of [all forms of] skinning is an illusion... a suggestion of a reality [the buttons do not actually move INTO the screen when pressed] that the trick to success is to find the right balance of pedantic detail and subtle suggestion .... something the Masters of 'our' craft seem to do effortlessly, yet others often miss.

The skinning I'm doing in FSX is predominantly 'modding' of existing graphics....and almost all of those are essentially 'flat' though the better models allow alpha channels, bump mapping and specular shine, all in 'DXT5' format - editable as bitmaps via the appropriate extraction proggy into PSP.  It's quite complicated, particularly when the skins are very much 2D but applied to a 3D model....

....but it's fun.

To cut a long story short [too late]....as Snowman often reminds us.....

Skinning is supposed to be fun.

It's also therapeutic...