Ad Spots
You could put something in them, like ads, or your mission statement, or anything you want to show up on pretty much every page.
If you do want to put up ads, you're probably going to want to use some kind of ad manager as they are just divs.
Alternatively, you can just make them go away by using some CSS like this:
.portholes {
display: none;
}
It's important to remember that the banners are only shown to newish users, so you will probably want to browse your site logged out so you get the anonymous experience to test your banners.
Logo and Favicon
admin->theme->Logo and Favicon</tt>: Upload some pictures and change them.
The system does not scale/crop/rotate or perform any contortions to make your logo fit the layout. If you want your logo to fit the layout, it should be in the ballpark of 250x70 250x69 pixels if you upload something a lot bigger, or a lot smaller, it will probably look kind of funky. Maybe that's what you want, if not keep use your graphics editor to size it around 250x70to 250x69.
Look at your logo in context, and make sure it's aligned. If your logo has a lot of text in it, it should probably be centered with the row of buttons next to it.
FAQ
The site's FAQ is a static page (under admin->content->Static Pages) which uses StackOverflow's FAQ as a template.
You should read through it and make it your own... or at the very least fill in the blanks (and in sites created on certain versions of the code, replace the string "%(domain)s" with something like your site's name).
Other Stuff
There's a bunch of stuff under admin->content->Html Customization you should look it over and make sure the verbiage is to your liking (The welcome message has a blank and the tag examples are: "tag another-tag a-much-better-tag". Both probably need changing).
As an aside, much like the banners, the welcome message is only shown to newish users so you'll need to browse your site without being logged in to see it.
