drupalib A place for library drupallers to hang out

How do sites that use a file manager such as IMCE or the file managers built into WYSIWYG editors configure the directory path settings? We're evaluating IMCE (using FCKEditor as an editor) and are not comfortable with storing uploaded files such as images embedded in pages or media/PDFs that are linked from pages in directories that incorporate user IDs, since we anticipate that a given node may very well have its owner changed in the future (use case: subject librarians change departmental responsibility). Do you put all uploaded files in one big folder?