As Mossie's #2 answer suggests, that's the answer.
You can do this "in real time" by opening the TCE window, then returning to the model in the viewports and selecting or deselecting any areas you want. Then, return to the TCE and move only the selected items to someplace else in the TCE.
It would help, of course, if you already had a graphic to move the various pieces to.
And, it just so happens that someone needed to get access to a tutorial I wrote on the TCE that's aircraft specific. And it's still downloadable online:
Episode 10: TCE
enjoy.