I'm getting my RPi today. Whats the easiest way to install? I've read over the HOWTO...will that install directly onto the SD card or will I have to navigate around a bit more?
Unfortunately, installing on RPi is the hardest one (but I think still easy)

You should follow steps from
http://cgminermonitor.com/GetStarted "Compile from source (e.g. Raspberry Pi)". Yes, it's install on SD card. Send me an email, if you will have any questions.
Can I run two instances of CGMiner on the Pi and monitor them both at the same time using this? I have one SHA miner and a Scrypt miner I have to run on separate instances I believe.
Sure, that would be no problem. Yes, you just have to run two separate instances - run them in different folders or set up different config name for each (as run parameters).
Possible bug:
Reported value of hashrate at CgminerStatistics per GPU (from graph)
is not the actual one reported by cgminer and the worker page (with "GUI" cgminer).
Example: one of my miners has 4x 7950 cards - each one does pretty steady 2.45Mh/s X15
(reported by both sgminer and CGminerMonitor worker page).
The graph reports 2.35 very consistently.
Suggestion: There might be some faulty conversion - x1024 instead of x1000 or vice versa?
Thanks for reporting that, I understand that on worker page everything is correct, but on Cgminer Statistics page the value is a little lower than it should be? I'll look at that.