Generally PR is calculated for each page separately. It depends on the links to that page. So typically a page 2 levels down in your structure would only have links from your own site. If you link from your home page directly to a second or even third level page is gets the same amount of PR as a page in the first level.
If you have important keywords in a page in the second level you could therefore link directly from a page in your site with high PR.
But: for good ranking often the raw PR is not the most important thing. If you have a page in the second level, and you link to it from several other pages also in the second or third level AND you put the keywords in the linktext, then that page can gain very good rankings.
It's a question of how to set the site up in general. There is the concept of passing PR from high pages to low pages. But also very important is the concept of themeing your site. The linking within your site should be set up so that links always carry the keywords of the page the link points to.
I would suggest to do some reading in this (Link Development) forum. There are some very profound and valuable strategies laid out.