Casey,
I just recently installed Acceleration on one of my FSX setups and it screwed up my terrain.cfg. When I loaded FSX I had no water showing anywhere for some reason! Panic time. Poking around I discovered that the install overwrote my existing one. Fortunately, I had recently backed up my entire FSX partition and was able to pull off my good terrain.cfg, stuck t in and all was fine. Funny thing is that my other Acceleration installs went with no problems. Go figure. As I recall, you'll need to uninstall SP2 before installation. To be safe, I'd do a total FSX backup before installing ACC. I'm sure that if you Google Acceleration FSX install, you'll get lots of tips before diving in.
One more thing: be sure that you backup your FSX.cfg because you'll get a new one during the install.
Note: Just saw Rod's post as I was writing this. Sounds like he had a slightly different experience with a few things than I had, so if you back everything else up first you can start from scratch again. (I don't remember having issues with Tongass.)