I have never tried using ProRes or DNxHD for editing in Premiere Pro. Does it work?
If not, you may want to consider an intermediate codec from Cineform. I used it for many years and just stopped when I started shooting with my new camera which doesn't require it.
Cineform is good for cross platform use, and the way it works, using wavelets instead of Macroblocks, is superior to anything else I have seen.
Your last statement makes me feel confused about what you actually want to know...
There is no such thing as an intermediate codec for PrPro. PrPro works with source footages from the majority of cameras natively. PrPro also supports all intermediate codecs generally used in production. Some of them like DNxHD require separate installation into your OS.
That means you can easily import those ProRes and/or DNxHD intermediates you supply your editors with into PrPro and cut your own project out of them. Or you can import your PrPro projects within which you stabilised your source footages or particular sequences from those projects into your master PrPro project, cut your movie out of those sequences, delete what's unnecessary so that your master project doesn't blow and rerun Warp Stabilizer (personally I'm not a huge fan of which)...
I use Mercalli to stabilise my wildlife clips where I was unable to use a tripod, and to keep things simple, export the stabilised and colour-corrected clip as a "lossless" intermediate file using the free download Avid DNxHD codec. This produces a high quality .mov file. I then import these stabilised clips to my Premiere project and replace the originals with them, saving with a new project name.
On the Avid site, there is a useful guide to using intermediate files in this way to avoid projects becoming over complex - or in the case of the Warp stabiliser seriously overweight!
I use a PC, but this workflow should be fine for a MAC. Some people may suggest using UT or Lagarith as intermediate file codecs, but these are PC only as far as I am aware.
In the case of your own project..I would only process ( add fx) to the part of the clip as used in the locked off edit.
I would probably make a D.I with handles to do this.