I am a regular InDesign user and very familiar with publishing long documents, so I'd like to reassure you, you're not mad.
It appears you can set the page numbers in Bookwright to only start appearing on a certain page, but the running foot (probably the title) appears on every page, including the cover and front matter, where they definitely don't belong.
I've tried covering the unneeded footers with text and image boxes, but alas, you can't change the fill color on either container, so you can't cover them with 'white/paper' overlays. There doesn't appear to be any functionality to individually select the footer...
InDesign is no great prize when it comes to setting footnotes, by the way. They don't import from Word; you'll still have to set them manually. But at least with InDD you can type style the text boxes to the font and so forth you want for all notes so they format when you paste the text in.
Bookwright is more powerful than, say, Shutterfly, when it comes to managing long blocks of text around photos, but it's not a "real" book publishing software until it can offer more customization of standard features.