I've been using it for about two years now, no idea how to fix your problems. As for finding your settings, it's all preference really. The only thing I can recommend is if you were a high sens player before using accel, set up your driver so the sensitivity cap is your old sens (easily done by changing post scale to something <0 and making sure "Scale sens cap with post scale is checked). This allows you to keep all your muscle memory which is pretty ownage. Second thing I can recommend is finding out how "fast" you move your mouse when you flick so you can make sure your sens hits the cap a bit before that. If you've figured those things out just keep them consistent and you can fuck around with the other settings until you have something that feels good. Play pubs with it for a day or two and you should get used to it fairly quickly. Kovaaks videos are pretty decent at guiding you through the setup anyway.
Does it help? Depends how you aim really. If all you do is flick (which in TF2 you can get away with more than in other games), using mouse accel is basically pointless. If you're struggling with tracking though, having properly set up mouse acceleration can help you improve a lot. The only thing that gets slightly negatively affected by using a low base sens is long smooth airstrafes but you can find settings that still work fairly well for doing those.
Overall I'd say the biggest drawback to using the mouse accel driver is that 98% of your friends will take the piss and call you edgy.
Only question I have is how do I get this to start minimised? It launches on startup as I'd like but I'd rather not have to minimize the GUI everytime I boot my PC.
-m as launch option on the gui