Yes. Except you need to make UVs for the lowpoly parts, and those UVs need to match the size of the intended output. If you load your registration marks into UVW Unwrap, as a background bitmap, then you can adjust your lowpoly UVs to match. Then you can bake the polypainted models into the lowpoly UV layout.
Ok I think I understand what you're saying, so it doesn't matter if the size of the UV for the lowpoly fits in the 0-1 UV space just as long as it matches the texture I import into the UVW Unwrap it should work? P.s. Thank you for taking the time to help me get this figured out, I really appreciate it.