Empgamer: I've got the same issues with WM6,1 as you described. I'm genuinely amazed that Windows Mobile syncing to windows (Vista, so no active sync for us) doesn't work out of the box when managing edited documents on your PC & PPC. The PalmOS, with Documents To Go, always did an excellent job of this. As for the notes, I can't even get Mobile Office OneNote to sync with OneNote on my PC! What's the point of that?
Anyway, I'd be very curious as to how you solved your issues; I'm currently spending countless hours trying to get the functionality on my Windows Mobile device that I took for granted on PalmOS. (BTW, DocsToGo doesn't support syncing on Windows Mobile! Seriously, that's one of the main things DTG had going for it. I'll never understand what developers think when they come out with these products.
Motorola Droid Bionic
[AOSP ROM] Unofficial CM10/JB ROM