I have 1200 pics on camera roll and 900 on photo stream. 1. why are they different? 2. if all are supposedly backed up on iCloud if I delete all photos on my phone will they still be on iCloud or do I need to separately download them to my pc first?

Photos are only uploaded to iCloud after photo stream is enabled. It's possible that you already had 300 photos in your camera roll when you turn it on so they weren't uploaded. Also, photo stream also only maintains photos for 30 days, although earlier photos already streamed to your device from photo stream are not deleted. If you had turned photo stream off, then back on, and the 300 photos fell outside of this 30-day window at the time, they would not be in your photo stream album. (FYI, photo stream will also only save the last 1000 photos.)

If you delete the photos on your phone from the camera roll album, photo stream will be not be effected. If you delete them from the photo stream album on your phone, they will be deleted from your photo stream on your phone and any other devices connected to the same iCloud account/photo stream.

To keep your camera roll photos permanently, don't rely on photo stream as a backup. Import them to your computer (http://support.apple.com/kb/HT4083).