Different Template for subpages and Archives

I have a site where the homepage look and feel is different from the subpage design. WP is the driving force behind the news feature on the homepage.
What I want to do is have the homepage display the most recent post with a link to an archives directory page. The /archives/index.php would have the list of archived posts and when clicked, they would appear in the Subpage (Archives) template.
From what I’m seeing, you can only create one template in WP. When I drived to copy and paste my root index.php folder into /archives/index.php and modify it, I just get a blank white screen.
The other thing to keep in mind here is that I would also like to take the listing of links and put those onto another Subpage design under /links/index.php. Again, I’m running into trouble because I would like to use WP to manage these links, but I can’t seem to get it configured to work under a subdirectory because my WP install is under the root.
I’m not really that familiar with PHP, so if you have thoughts, please let me know. I’d really appreciate it. I know you can do this with Moveable Type, but I’d much rather use WP.
Thanks!