After Effects is a compleatly different program, all effects and compisition you do in it will be done outside of final cut and must be rendered to new files which then can be used in final cut.

Work Flow works like this
Edit
Export clips you need effects on
open those clips in AE
do what you want to them.
Encode the Effect video files out to new copies
And then Reinput the new copies over the old ones.

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