Is there any way to have GUIMiner-scrypt start/stop on certain events? I would like to be able to to run something like a batch file command and macro it to switch over profiles for mining; full throttle at idle, moderate setting for some games, and off for gpu intensive ones. Ideally mining would be throttled by resource usage or if a an exe is loaded but I can't code so I can't tweak things.

And to mine both Bitcoins and Litecoins I just need to have two cgminers open and connect to each respective pool, correct?

This feature would take a lot of time to implement and isn't in the works for now; the easiest thing would just be to stop the miner, lower the intensity, then raise it again later when you're doing something else.
To mine litecoin and bitcoin you'd need to have this guiminer and the original bitcoin guiminer open at the same time, then make a cgminer tab in both programs and run them. I have no idea what kind of hash rates you'll get with each, though.