Hi Walter
Definitely After Effects is the way to go.
I wouldn't recommend Encoder neither Compressor.
There is not an "Auto" for RAW CR2 files, you are developing a Digital Negative, which like a Film Negative will need its own Develop process settings for each sequence.
If you are going for best quality make your AE project work with 32bit ( I prefer and work in 16bit. It is enough since RAW CR2 is 16Bit)
When you import each CR2 sequence to AE the Adobe "Develop" Dialogue will pop up, you can adjust your settings there, you can recover a huge amount of highlights and shadows here, like 3-4 stops on each one, and make it pretty flat (Log-c like) so you have tons of information to grade it later. It is crucial to not auto adjust each sequence in this step, because same settings can create undesired results in different shots.
This is not like RED RAW, CR2 files actually can handle way more information, and just by developing them correctly you can recover a lot of information. Like a sky that was completely blown out, and after develop and highlight correction you can see its blue color and clouds back again.
If you don't want to change the resolution of the file and use the original one, just create the AE sequence, from the file sequence imported, right click it and pick create new comp from selection.
Check frame rate from the file you just imported and on the comp. a different frame rate on this ones will result in possible issues.
finally send the comp to render and pick DPX.
you can render out 10,12, or 16 Bit DPX sequences in log or linear
pick what you desire on the dialogue box
Don't forget to check on Main settings - Depth: Trillions of Colors
if you decided to go for 32bit workflow, which I feel is kinda insane
you can export 32bit Tiffs too, here don't forget to pick on Main setting Depth: Floating point
some final recommendation on the develop dialogue settings:
when recovering shadows check frame at 100% resolution, because sometimes when you are recovering you can introduce undesired noise, that when not watching at 100% is not visible.
Second: go to detail tab and reduce sharpening to 6 or 11, the default is 25 and this setting is way too high.
Remember you can always go back and change the develop dialogue settings by right clicking on the file in the project window and chose interpret footage/Main and then/ more options.
All the setting from the Develop Dialogue are saved as a metadata file on the respective CR2 files folder
So for the next shot you can load those setting in the Develop dialogue, so you don;t have to start from scratch on each sequence.
Just so you know one frame 5K CR2 Canon file translates into a 119megas DPX 16bit 5K file
That is why I usually go for the traditional 10bit DPX or Apple Pro Res 4444 if it is a lot of footage
Hope this helps, let me know if you have more questions
Caryl