>Anyway, what I haven't been able to figure out is how to make the command window not always be on top. I tried checking the context menu, but there doesn't seem to be anything there. I also gave a rather quick look at the Options dialog, but there didn't seem to be anything there either.

Right click the titlebar and turn off dockable.

>And what's with that "stripe" down the left side of the code window?

You can add Breakpoints, Bookmarks and Tasks all in the margin. Its setable in the Options Dialog.