I am sorry for all of these questions but I cannot figure out how to make these work...

I installed IP onto my database.  When I installed it I installed it into a directory.  I then moved ALL the files out of that directory and moved it into the root directory.  Therefore my domain directs directly to the site.  The problem occurs when I try to change pages it directs it through the old directory and turns up a page not found error.

To solve this I tried to reinstall the files under the root directory but it did not fix the problem.  Where could I find the code that is directing everything to this old directory??  Thanks.

Sounds like you need to change the value for script_path in your database, that will be in the config table (phpbb_config) if you didn't change the prefix_ when installing, use phpMyAdmin (or whichever sql admin tool your host provides).