Yes, ProRes is way to go. You should let FCP do the conversion, ideally whenever you create a new project there already and import the files. You could do it in AE of course by running a conversion render, but this is always prone to introducing errors like Gamma shifts or messing up your source tiemcode.
Could you explain how to do a conversion render? Maybe I will give it a shot? As a test because that would be my prefered choice.
As for letting FCP convert, how do I reconnect the layers with the new footage? Thanks!
Is there an easier to use format than ProRes? Maybe animation? Thanks!
> Could you explain how to do a conversion render?
Drag a footage item into the Render Queue panel. Set the output module settings for the render item to whatever you want the output format to be.
from After Effects Help:
"To create a new composition from a footage item and immediately add that composition to the render queue, drag the footage item from the Project panel to the Render Queue panel. This is a convenient way to convert a footage item from one format to another."
If you're new to After Effects, please start here: