Well glad you got things setup! I'm swamped at the moment and flying to Canada tonight (well at least starting the journey to the airport) so won't be around for the next week however if we don't get things straightened out today I'm sure one of the other guys will have some good advice
I don't use the notifications at the moment and haven't tested them since XBMC 11 and since you are having the same issue as Kat I'm wondering if its an issue with the update? If I get time today to remote home I'll take a look and see if it still works for me.
1) You don't HAVE to use nzbmatrix at all (manually) - I use it for grabbing non movie/TV stuff and adding it to the SAB queue either by downloading the .nzb file into the 'watch' folder you set in SAB and it auto adding OR by just copying the URL and pasting into the add box within SAB.
2) Indeed. Just add any movies you want into CP set at whatever quality you want it to look for. It will use the NZBMatrix library to search, download and then rename/move (if setup) to the correct location and notify XBMC to update its library. Simple
3) Yep same with SB. Just add in the shows you want, set the episodes you want to 'wanted' and it will go off and search the index sites you have setup in the config for the episodes, download them, rename them, move them, grab the pretty pictures and then tell XBMC that they are available to watch... Well they would if your notifications were working.