After you set up the master folders on the server, you move what might have be in separate locations on different shares or PC's and place them in this centralized location in a more logical order - in folders associated with their profile or fund. This is not meant to be a replacement for a robust document management software. 

To find a document you need to know where to look.  FIMS will facilitate the organization, but regular Windows Search or knowledge of what profile or Fund is associated with the document is necessary to find the document. If you need fast retrieval, zipped or compressed document storage and a flexible and fast search capability with the ability to tag individual documents/files with key words, then you need a different solution.

If you need a way to manage the plethora of documents hiding on various PC's, shares, folders and subfolders so that there is some logical place to put them, then the fund and profile folders will be fine. The added advantage of the fund and profile folders is the myriad of macros that can be run against your merged documents to split and file them in the appropriate folders.