1. Set a different material to all the faces you want to be using a different texture sheet, then you UV thous faces as you would normally, just ignoring the other material(s) (can work with only that material by selecting thous faces (simple way, select material ID) then with them selected in face mode, apply the UVW unwrap modifier and you will only work with the selected faces.
A quick example here would be the Z-9WA, where the white material is UVed to the first material sheet, which is the Z-9 sheet, and the blue material is new/modified parts UVed to the Z-9WA sheet
2. Personally to start off with on anything that I haven't made with a spline or anything that isn't already properly UVed to start off with, I take all the faces that are not and then do an automatic map on it. This keep in mind is throned upon if you ONLY do this as these UVs will be very unoptimized and badly packed etc so they need to manually fix them up on top of this, but it gives you a pretty good base to work off I find.
Do this by first going into your UV window, then select the face selection tool, select all faces (ctrl+a), then Mapping > Flatten Mapping and then I personally always UV in non-normalized mode, as then its much simpler to UV everything to the same pixel ratio to start off with, so uncheck the "Normalise Clusters" button and then you have a decent base to work from, then from there you just need to stich UVs together that need to be and pack them up into a nice UV, then once your 100% done with all that, scale the UVs down/up (pretty much all the time you need to scale them down) to fit into the UV borders
maybe a quick hint or two would be great