I've spent ages going through clips in premiere and trimming them, etc...
I've also renamed all my library files along the way so that I know what is what. When I copy and paste these layers from a premiere timeline into After Effects to begin working on FX for them they paste over with the original filenames instead of the ones that I've spent ages categorising.
Any way to get around this? Seems weird to me that layer names don't remain embedded...
To my knowledge, Ae can get only the sequence names from premiere, the layers will be in their original name. I tried fiddling around but could not find any way to get out of your predicament and the only advice I can give you is to consider what you are set out to accomplish here. if there are so many imported layers that you need to keep track, you might want to reconsider your workflow. for example, do you really that many layers edited together from premiere to an after effects timeline for vfx? let me quote one of our Community leaders Rick Gerard:
After Effects is for creating shots, not editing movies. Especially when you start out you should limit your After Effects compositions to one shot, render that shot, then do your editing in a NLE like Premiere Pro.
maybe if you provide more workflow details then this could help us to help you.
in any case, if you feel this is a feature worth having - please fill this form in order to make Ae better for all of us: Feature Request/Bug Report Form