I’m using two copies of EE, one on my server installed by pMachine, and one at school installed on a Windows server by the tech team there.  I paste code from my site into the school’s site, change the file names, and sometimes can’t get the template to load properly.  I start to suspect that the school copy was installed with a different file structure Here are one clue: 
When I call the control panel on my copy of the software, I get this URL:
http://www.mycopy.net/mycp/index.php?S=11b66f7bd75c96cd2b151153cf08f7ce61425e38
which gives the control panel (mycp) and the index file that runs from it.
When I call the control panel at school, I get this URL:
http://ee.myschool.edu/schoolcp.php?S=a5f1369a4abcf8a36588b0ef14f106fa1adec0ce

I first noticed the problem, though, when building archives and categories pages at the school site.  When I tried to view these new pages, I was sent to the site index page instead of the index page for the new blog I was creating. Thanks for any suggestions.

It looks like the school installation might be using masked access to the Control Panel.  That shouldn’t cause any problems, though.

> I paste code from my site into the school’s site, change the file names, and sometimes can’t get the template to load properly

I don’t really understand what you’re trying to do here.  What sort of “code”?  Where are you pasting it; in a Template or somewhere else?  How does it not “load properly”?  Errors?