How to put edited AE clips back into PPro? (CS5.5)

Okay, so, here it goes.
I edit my main footage in Premiere Pro. I recently purchased a denoising software that only is compatible with After Effects, so I have been using the denoiser plugin in After Effects. After I edit my basic video cut in Premiere, I select all of the clips (including audio) in the timeline, and open it in a new AE comp. After it has been opened, I do all of my major video touch ups in AE (such as denoising). Now, when I try to export the project as a Premiere Pro (PP) project and open it in Premiere, it doesn't load the project. It's just an empty sequence. That is not a big deal though, because I tried something else. I tried linking the AE composition from AE to PP which works, but it is very slow and precomposes all of the individual clips into one video clip.
So, just to go over it again, this is what I did: Cut clips in PP > Selected all clips in the timeline of PP and opened them in a new AE comp > Edited the individual clips inside the AE comp w/ effects that are not supported by PP (only AE supports the denoiser effect) > opened the edited AE comp in PP > then the comp came up as a precomposed video clip instead of individual clips.
So, my question is, how do I get the comp from AE to stay as individual clips when I open it in PP in case I need to adjust something? Is there a way to do this? Or should I just do the denoise effect very last?
Two other things:
(1) I noticed that it is extremely slow in PP to render parts of an AE comp... is it just because of the added effects?
(2) I transcode my video footage to ProRes 422 before I bring them into PP. Once I bring the clips into AE and then back into PP (if I figure out how to), will the clips still be the same ProRes codec? I need them to be the same codec due to color grading and effects later on in post.
Thank you SO MUCH if you can answer this! ANY help is appreciated! I explained this pretty much as good as I can, so if you don't understand my question, just ask, and I'll try to give you more info. Thanks!!

I select all of the clips (including audio) in the timeline, and open it in a new AE comp.
That's where you messed up.  Instead, right click on each clip you want to fix, and choose Replace with After Effects Composition.  Then redo your effects.

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