lets say i want pages in /folder to rank, would I get links to the folder rather than the homepage, which links to the folder? Or can I just get links to the homepage?
When building your linking structure, try to keep all pages within 2-3 links of each other, no matter how many pages you have. Not only will it make it easier for users to navigate your site, but the search engines can find their way around more easily too. If your linking structure is solid, your pagerank is spread around. If you have rank on your homepage, link to one of your pages in a subfolder, and the homepage will pass a small amount of rank to it.
Yes, this does work... but be patient, it may take one or two more PR updates for your inner pages to be assigned a pagerank. So far on my directory, (the popular one, hehe), most of the sub-pages off the main page, are a PR3, the ones after that are PR2 and so on. This took a year, maybe I didn't advertise enough or that's just how long it takes... Also, links from other high-PR sites to your sub-directory should give your sub-directory a little more weight as far as PR in my opinion anyway. So if you have a particular sub-directory that you'd like to see get a higher PR, promote that. Note that most web-directories won't accept subs unless in a deeplink enabled submission. As far as paid advertising on sites, publishers will usually let you advertise a sub-cat/dir as long as you pay