Here's what I do:
Open the footprint editor, create new footprint, and set the grid to something useful, like 5mils.
For each footprint, I have an enclosure internal wall outline, external wall outline, and screw locations (all in User.Drawings layer).
I mark the center of the enclosure as both the grid center and origin point using this tool:
Plot all centers for all controls, switches, etc. on the footprint using line and circle graphics (also in the User.Drawings layer).
Make sure that there's no text on the footprint that's not in the User.Drawings layer. Edit the footprint attributes so that it's not included in the BOM, etc. using settings like these:
Save the footprint for later use.
Build the project's schematic, assign footprints*, run ERC, etc. until it's where it needs to be, then open PCB new.
*Make sure that the footprints you're using for potentiometers and other controls are shaft-centered, not pin-centered. Also make sure that your grid in PCB new is set to a value divisible by the same grid that you used for the layout footprint you created (5 mil is often the smallest I go for TH stuff).
Inside PCB new, click to add a component. Add the new layout footprint created earlier.
After placing the layout footprint, go ahead and mark the center of the layout footprint as both the grid center and origin point using the same tool used in the footprint builder.
Then, updating PCB from schematic, it brings in all of the footprints, select the footprint and drag it to the point marked for the control in the footprint builder. Click the component, type E, and check to make sure that its coordinates are in the right spot.
I hope this helps!