Hi David, the .MRK files specify which markings for what country are to be used for a specific plane, they can be opened in notepad and in this instance I'm using the Spitfire MK1a set for GB, as an example and should read something like this.
Common]
country gb
period P_1939_1041
branch Army
background SpitfireMkI.jpg
[Markings]
GB_Roundel_Type_A 0.1167835 0.5345702 0.110825 0.110825 0
GB_Roundel_Type_A 0.5837377 0.7013204 0.110825 0.110825 0
GB_Roundel_Type_A1 0.3231447 0.3050553 0.08071069 0.08071069 0
GB_Roundel_Type_A1 0.3230649 0.07125527 0.08071069 0.08071069 0
GB_Roundel_Type_B 0.3565553 0.6989263 0.1222319 0.1222319 0
GB_Roundel_Type_B 0.8226124 0.5416936 0.1222319 0.1222319 0
GB_FinFlash_Shape_5 0.1255758 0.1379337 0.09519536 0.09207297 -3.141593
GB_FinFlash_Shape_5 0.1258596 0.2401211 -0.09519536 0.09207295 0
GB_Num_SquadronCode 0.2472797 0.3046574 0.07637118 0.05727838 0
GB_Num_SquadronCode 0.3998094 0.05874956 0.07637119 0.05727836 -3.141593
GB_Num_Tactical 0.3821226 0.3199628 0.03819535 0.05729302 0
GB_Num_Tactical 0.2632982 0.07333601 0.03819535 0.05729302 -3.141593 LOCKED
GB_Victories_A 0.5001303 0.0530588 0.05075502 0.05075502 -3.141593
GB_Designation_Number_Wing 0.1934813 0.3080352 0.07101311 0.02130393 0 LOCKED
GB_Designation_Number_Wing 0.2079452 0.07036155 0.07101309 0.02130393 3.141593 LOCKED
The skins are made up of several layers, like an onion each one in game has a specific order in which they are layered, unlike the nice and simple IL2 there's a lot more to play with, that said you have a lot more creative freedom.
Now some of the skins come unlocked as standard ie Spitfire, this will give you one basic layer to play with which like IL2 is probably enough, you can open this up in Gimp and paint away to your hearts content, bear in mind though the game will add the other layers on top of your nice fresh skin, ie weathering, panel lines etc.
The real meaty bit comes when you have unlocked the skins using the kegetys mod
http://www.kegetys.net/ the readme will explain.
Once run and dumped out you will have access to all the skins and their layers, concentrate on the .DDS files and you can either use a separate program like DXTBMP to convert them or use the Gimp DDS plugin that will allow you to load them up in Gimp.
http://registry.gimp.org/node/70
The three layers I work with are:
M-diffuse0.dds = main skin
M-overlay0.dds = Panel lines etc
W-diffuse0.dds = Weathering detail
Combining all three layers in your skin of various opacities is a good starting block.
Have fun.