Turambar, I just happened to see your other thread, so I know that you've already got past the part you've asked questions about, but for the sake of the thread, I thought I'd answer here anyway. Sorry I did not get back to you sooner. For myself, my gaps were very minimal, so I didn't fill them in with anything. Also, I had a plexiglass cover, so the small gaps would not really present a problem then. If I were not going with plexiglass, then I would recommend filling in those gaps. And yes, I would use bondo personally.
Also, for my other control panel, where I used the self adhesive artwork, I did prime it first. I primed and sanded it a few times to give it a super smooth, even surface to stick to. But depending on what material you're using, you may not need to. But I would prime it, yes.