To avoid Front Page messing up pages I create and maintain without it on a site, I've been making separate directories for those pages. Now I'm finding FP folders and files making their way into my separate directories when the web designer updates the rest of the site.
Is there any way to keep those out so sections of the site are kept separate, to avoid damage?
you have to do it by hand - if you make a web in FP it creates those folders - it has to. It's easy enough to avoid them when you are uploading but the problem comes in when your client gets involved. You'd have to train them how to do it the way you do it.
That said those folders aren't going to hurt anything just sitting there.
I never recommend using Frontpage for uploads, and therefore, never using their extensions. Even if you must use Frontpage or a webmaster of yours does, I recommend building everything locally and only uploading the necessary files from the local filesystem.
Frontpage tries to simplify everything but mucks everything up in the process.