> “Ultimately my goal is to just have certain overlays (like scratches and burn marks) to be visible on the film but not the background of the overlay to make the source film either lighter or darker (I want it to be transparent). “
Make the overlay track a parent of the source footage (Parent/Child relationship). Place the other clips on a separate track.
> “Also, on a side note, is there away I can link audio and film clips together so that they always stay together when moved?”
Group them (select and press G)