Yepper. That's exactly what I said.
There may be a couple places in like signup or whatever that it might be hard coded. I don't remember off the top of my head. If there is, you'll know it off the bat.
Here's an example.
Add a theme to your site. Make sure if it is a duplicate theme of another on your site, that you edit the style sheet (the theme name) so you know it's your specific home theme.
Go into the site admin area, then select the main blog. On the right, add the theme so that blog can access it.
Activate the theme for the main blog as normal under presentation.
Start customizing.
As a not, by default activate and signup files don't include a call to a sidebar, so you may need to add it if it jacks up your theme.
From there, you can home.php, page template, and edit all you want.
The WP template system is so flexible, anything is possible. I frequently code up a full page template, including content, then create a page in the back end. Then select the template, give it a title (for the head section of the document) and a slug, and it's ready.
I've used this extensively on my blog, and I do mean extensively. Templates for pages, sub pages, all kinds of neat stuff. My code sings, and the blog dances a jig. :)