FMDesktop will work with whatever your standard is. If you use AutoCAD (or any AutoCAD based product) with Facility Link, you can set these up as you desire. If you use Architectural Desktop or AutoCAD Architecture (without using Facility Link), you can set these up in the Spaces. If you use Revit, you are somewhat limited in that you can specify Centerline or Paint to Paint; you can't do BOMA as of yet.
Face of Wall (or Paint to Paint as some refer to it) is probably the easiest. It has a couple of benefits in telling you the actual size of the room (flooring measurements for example). The only drawback is that there is "extra" space that is unaccounted for on each floor plan (the space between the walls).
Centerline to Centerline is another approach that a lot of folks use to account for all of the space within a building.
The 3rd common option is the BOMA standard. This accounts for space based upon the "type" of space. So, for example, a polyline between an office and a corridor would be located at the paint side of the corridor. That same office might be next to another office which in turn would be in the center of the wall. Its a complex approach and takes time, but the biggest benefit is probably in charge backs or leasing environments where space is to be "maximized".