A word of warning first. Whatever you try to import to Pro/INTRALINK, do it through the Pro/INTRALINK Client UI. Bypassing the UI could cause database corruption.
Importing non-Pro/E objects can be automated using Pro/INTRALINK Scripting. From the Pro/I Client select [ctrl]+s to access the scripting interface. Pro/I Scripting records key strokes similar to Pro/ENGINEER mapkeys. The picks are recorded in Java so you can easilly expand the default functionality.
Like trail files, PTC only implemented this technology to help replicate software bugs. But I've gotten it to do quite a bit that PTC never thought about doing.
You can write a simple script to loop through a series of folders on the hard drive and import objects. You can even set the attributes for these objects and automatically check them in. Pro/I Scripting supports completely unattended sessions. A script can be called from the Pro/I Client startup command.
As far as I know there isn't a manual for Pro/I Scripting. But if you know how to program in Java, you won't have any problems getting it to do what you want.