Are you doing the editing in FCP? What are creating the 3d animation in? What resolution footage are they giving you?
If you have the 24p raw footage, I would work at 24p until you are finished with your project, then have the whole thing downcoverted (which will in turn have a pulldown added to it for broadcast and run at 29.97).
You can add interlacing in AE, but I need to figure out what step of this process you are actually doing first.
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