How do I combine the preloader transition with the preloader percentage bar?

lol. yes, _root is the main timeline. everything is on this timeline, in some way or another. eg:
_root -> movie1
_root -> movie1 -> movie2 -> movie3

you see?
As to answer your question - “would that be part of the problem?” - who knows? how exactly are you using as in your scripts?

a bit more information would be useful :).
if you get stuck, there’s already an example there with the completed preloader bar + transition. you can use it as an example of how to do it.