Like they said above you need the SFS extractor, you can download it here;
SFS Extractor v2.0 BETA 12
Next using SFS extractor your have to search though the fb_3doxx.SFS files for the ship you want.
(hint; click on path in the SFS extractor to make it easier to find the Ships dir, like ton414 pointed out 3do/ships/)
Once you have found the ship you want, your need to look for any *.tga & *.tgb files and extract them.
After you have extracted them you will need to re-save / convert them as Photoshop will not open them as they are, don't know about gimp. To do this you will need this program;
IMF Viewer for TGA conversion
Once you have converted them your good to go.
(note; your find that the main ship skin is in fact 8 skin's at different resolutions;
skin1o.tgb & damage1o.tgb = 1024 x 1024 < not all ships have such high res, tends only to be battle ships and carriers
skin1o.tga & damage1o.tga = 512 x 512
skin1p.tga & damage1p.tga = 128 x 128
skin1q.tga & damage1q.tga = 64 x 64
skin1x is the clean skin and damage1x is the damaged effect skin)
(hint; this might be oveous but to save your self time open the highest res skin for that ship and make your changes, when it comes to save it just resize you image to the desired resolutions)
Once you have made your changes and saved your files your want to see it in game, to do this go to you "MODS" folder which you should have in your "IL-2 Sturmovik 1946" dir, once in the "MODS" folder your have to crate a folder ( call it what you want ) then in this folder create sub folders like this 3do/Ships/ *name of ship* ie if it was the carrier HMS Illustrious you re-skined it would be 3do/Ships/HMSIllustriousCV .
Then move your ship textures into the into that last folder ie the HMSIllustriousCV folder and run the game.
Done!