Not sure I'd use Compressor. It doesn't have the ability to actually insert pulldown (which is what you're want to do) and instead attempts to create new frames. That's great for slo-mos but not for this. Of course, if that's the only tool you have, hey, you gotta work with it.
If you have access to a recent version of After Effects, it should do a much better job at
introducing 3:2 pulldown so that your footage runs at 29.97.
Not entirely sure about the conversion to 59.94 though (as I've never had to go that route myself with a digital file), hopefully this post will serve to bump this thread so you can get specific advice for that.