Yes, you can add missing vehicles to a skin mod after you have been working on it. You just have to do it by manually adding the directories, burn settings, etc. I recommend checking out eliw00d's tutorials since he covers all of those manual steps very clearly. Just pay special attention to the structure and naming of the directories. I generally open a second mod in the same session which has the full set of vehicles so I can double check the naming.
tutorial link:
http://www.coh2.org/topic/35805/tutorial-setting-up-a-skin-pack
If I am making a skin mod and I know that my goal is to provide a skin for every vehicle, I create the entries for all the vehicles right from the beginning. The first build will take a while, but after that, each build only spends time compiling the specific maps which are newer than the previous build. So you can iterate on one or two maps or vehicles at a time and not incur any real hit in build times for the rest of the vehicles which you're not currently touching.
The two German factions use vehicles from each other. Yes, the same models. Some of the other factions (US, Soviet, Brit) also cross-reference one specific vehicle here and there, but the Germans use quite a few. If you only want to do a skin for one of the two German factions, then you will have to manually add those cross-referenced units from the other. On the builder tool, you need to put them under their own original "armies" directory structure. Many modders who make German skins have simply taken to always making the skin support both factions fully, since it's not that much more work.
The other map types (normal, spec, gloss, alpha) are optional. I believe if you don't explicitly provide them, the skin will use the default ones in the game. You can generally skip them if you're not trying to tweak details in those specific map types. One possible exception is the gloss maps. I find that the default gloss maps (if you don't provide them) are a very different value-wise between the various German vehicles. This means that diffuse maps with similar colors and values can look contrasty in some vehicles and washed out on others, making it difficult to get the same look across all the vehicles. Whether or not this is noticeable will depend on the specific color scheme you are trying to achieve.
Hope this helps.
Relic Entertainment
cblanco ★ 
보드카 중대 
VonManteuffel 
Heartless Jäger 
