Keep in mind that the "One Time Takeoff" will not save or remember any mapping
If at all possible try to tie all model components to an "Assembly Takeoff" and make a running tally of the items that need to be added to your timberline database so you can add these later.
Keep all of your exporting phases and scopes seperate. You can merge these files later in Timberline and it will remember where it came from.
EVERYTHING needs to have a unique name if it is in any way different from it's other components. For example, a 3'-0"x7'-0" door in Revit will insert both into an interior wall and an exterior wall the same. However, the costs for these two doors will be much different and they will be grouped together in Innovaya accordingly. A simple 3x7 HM Ext Door title to differentiate the two works fine.
Create seperate estimates that are the same name as the phase you are taking off from Innovaya, you'll thank me on your first update.
That's what I got, keep it real...