If you are going to working with Intralink-controlled files, be very careful not to go behind Intralink's back. Working with files contained in your '.proi' folder without updating your local Intralink database (local.ddb file) is the easiest way to corrupt your workspaces. Yout must use linked sessions of Pro/E wo work with Intralink-controlled data. Even then, never-ever browse directly into your '.proi' folder and work with files... pull them from the workspace.
If you wish to start a Pro/E session that is linked directly to an existing workspace you can use the command-line option (this is from memory, so I could be off a bit):
> proe2001.bat -wworkspacename
This assumes that proe2001.bat is your startup script. Note that there is no space between the -w option and the name of the workspace.
This starts up a linked session of Pro/E that will correctly work with your local database, but the Intralink client will not be running...
Hold on...
I just realized that I may be interpreting your posting incorrectly... If you are asking where, in the Intralink loadpoint, your Pro/E loadpoint location is stored, check <loadpoint>\bin\intralink.bat (assuming you chose the default startup script name). In this file are two references to the Pro/E loadpoint... change the paths here, and that should be all you need.
Then again, I could be wrong on both counts...
-Brian