I agree. Get the timing down in the editing app, nail down all cuts. Then add the graphics by exporting the relevant section (if necessary) from FCP with current settings (no change). Do your magic in AE, then render to the codec of the FCP sequence, otherwise FCP will have to render in the sequence … the exception being if you have to use alpha channel, to render to the Animation codec with AE.
Now … if you’re editing in FCP with a codec such as HDV or MPEG-2 (an interframe-compressed codec) you must convert it to a proper intraframe-compressed codec (P-JPEG, PNG, Animation, 8-bit 422, ProRes) before importing into AE. Then you should render to the same proper intraframe codec, and use something like Quicktime to convert that movie to the HDV/MPEG-2 codec if you want.
I hope that makes sense …