1. Connect my PC hdmi (video card) to the receiver hdmi and the flatscreen to my reciever? if so what settings do I need to make to see the pc picture on the flatscreen?
I would think this would be straightforward, but it may not be. Your display needs to handle the resolution of your PC through it's HDMI input. So, you may need to set your PC to output 720p or 1080i/p properly. The Onkyo should have no issues passing the video on this way.
2. the rs232 adapter; is that worth using for my pc, and does it allow a USb connection?
RS-232 is a serial connection typically used to control a receiver. It's not a USB type connection, but is typically used for external controllers or for setup software and loading firmware. Unless you have some specific need for it, I wouldn't bother.
3. I also picked up the Bose mass 10 system...I'm wondering if there are better systems out there for $999.00 5.1 channels.
Yes, for about $100 there are similar systems, and for $1K there are significantly better systems. Pack it up IMMEDIATELY, then ask in the speakers section what you can get for $800 or so - they'll give you seme $1K recommendations for sure, but that'll keep you from blowing your budget.
For under $1K picking something like this up will serve you far better:
http://www.definitivetech.com/loudspeakers/procinema/procinema_600.html
...or maybe...
http://www.aperionaudio.com/product/Intimus-422-Harmony-HD,23,35,35.aspx
There are many other options as well which are beloved on these forums.