I've not done any colour correction or grading yet, either, but as I understand it you send individual clips across to AE, which has more advanced tools than the editing program. I've read about the Colour Stabilizer which is able to adjust for flicker. I think that the basic correction, with clips alongside each other for checking, is done in the editor. Hopefully Nick can enlighten us!
Thanks, grecodan, for the tip on getting the structure on paper. I've written my workflow down, to understand it, but checking off the steps for each shot on a spreadsheet is really neat.