Your question is a little confusing. What do you mean by assigned folder?
If you are manually chosing the folder for new parts, the files will be checked into the specified folders. Once checked in, any additional check ins of the same part will put it in the same folder. The only way this can be changed is if you move the object to another folder.
If "assigned folder" means a pre-defined folder for all the new objects... Pro/INTRALINK 3.x has a preferences option to set the default check-in folder. I believe it is on the Check In tab of Preferences. It uses this folder if you didn't specify where to check in. The catch is all new files are put in this folder. The software isn't intelligent enough to determine different locations for different files (purchased vs mfg or parts vs assemblies). As long as all the new files are going in the same folder, you can use this preferences setting. Your local preferences override system preferences.
Sorry for the confusion - At my last company everytime I would "check in" a drawing the destination folder automatically defaulted to the folder assigned to the specific item(s) (i.e .prt, .asm, .drw etc). At my current job I have to define the destination folder everytime I check in a part.
It does not appear that you can get the appropriate setting in the Preferences/Check In Tab do accomplish this (unless I am missing it of course).
Is there a setting I can change to fix this or do I need the administrator to set this.