Not 2 Pass VBR. Use CBR to guarantee you are encoding at the rate you choose. There is no practical reason to export a comp from AE through AME. especially to h.264.
Render out vie the AE render queue using "Animation" or "ProRes (HQ)" then take that file and compress with AME if needed or work into your edit.
You might need to massage the render settings for optimal output, but as Dave mentioned it is next to impossible to help without knowing specifics.
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