Yep, there are a couple of tick boxes to remember so that everything saves as one, it's very instinctive, you shouldn't go wrong.
Don't know about multiple runtimes, I use one runtime with sub folders, it works better for me that way, and yes I did try multiples but didn't like them. I find using the small black triangle to navigate my sub folders much easier, but that's my personal preference.

Injustice will be avenged.
Cofiwch Dryweryn.