Depends on the apps. You wouldn't want to leave Entourage, Fusion, Parallels, that kind of thing running.
Yes, multiple partitions, no disadvantages.
No, you won't need to uncheck the "Prompt" option.
SD! backups are quite reliable. But we can only be as reliable as the environment, hardware, etc. There aren't really checks you can do other than to occasionally try to boot from them, and pay attention if there are errors.
We automatically exclude the things that should be excluded.
I strongly suggest
reading the User's Guide!
