Lost on application.cfc

Hi all,
I've used application.cfm for ages on our site (now in sustainment) and we have been moved to a new server using CF9. Our server dudes have "per application" settings in place where I can map my custom tag directory (works fine) but when I use application.cfc, I begin crashing on all my pages that use relative pathing.

For example, the first thing the application does is query an Oracle table to get security settings. This is located off the root in a folder (oddly enough) called Security. That folder has a subdirectory called queries. I bomb with an error saying that "<cfinclude template="queries/user_role_select.cfm">" is invalid and it cannot find the noted cfm file and that I have to set up mappings in my application.cfc file.

Does this mean that I have to provide mappings for every directory and subdirectory under my root folder? Surely not! If so, how can this be done and how would I use that mapping in my cfincludes? I'm really getting started with the cfc files late in the game so any guidance and direction is GREATLY appreciated.

Thanks in advance!