I do rough cuts of my graphics in premiere all the time. I used to use AE for that like you say you are, but since CC premiere is so awesome and easy to use I don’t bother cutting timelines in AE any more.
I co-worker of mine managed to get a premiere timeline into Avid recently so I definitely know that is possible. I imagine the workflow from Premiere to Flame is going to be a lot more supported than from AE to Flame. Premiere has far better options for exporting: AAF, XML, etc. After Effects really isn’t built for this. And in premiere you can bake in timecode and clip names virtually automatically, which I just used on a project where I pre-edited my graphics for someone who was finishing in Avid.
However I realize you probably already have timelines built in AE that you would like to send over. The cool thing is that you can just import those directly into Premiere and then export to Flame – I think that’s going to be your best bet.
– Spencer