Simple, well, in theory it's simple.
When starting up, CM would catalog the BMP sets. It would know there's a 1011.bmp, so it would check for a 1011-1.bmp, if that exists, it checks for a 1011-2.bmp, et cetera, et cetera. For quick battles, CM can assign BMP sets randomly but for scenarios, the player can set them by selecting Skin 1 through Skin X, where X is the total number of skins in the game for that model.
As to the camo idea, these would have to be completely different units using the same model because they would have different stats (They'd be more difficult to spot). Therefor, when creating a scenario, you'd add a 'Panther VG w/ Camo' and it would have the bonus regardless of the actual skin on the tank. Therefor, if you downloaded a fieldgrau Panther VG skin and assigned it to your 'Panther VG w/ Camo' model, the unit would still get it's bonus for being camoflaged, even though it wouldn't look the part.
The real problem with camoflage is deciding its game bonuses realistically.
Keep in mind I use the term skin rather than mod, though in the parlance of CM, the two are interchangeable.