When I need to put holes a certain distance apart, I usually temporarily make a new panel, place the first hole at 0,0, place the next hole at the correct X,Y position and then group them. Then, I copy the group to the original panel. In FPD, when you copy from one panel and paste into another panel of the same dimensions, the past goes to the exact coordinates as the original. Handy.
As for measuring distance between two holes on some existing piece. It's easy to measure from outside edge to outside edge, then subtract the diameter of ONE hole. This gives the CTC distance between holes.
To find the distance between two holes while in FPD, again I sometimes make a new temporary panel, copy the group to the new panel (without disturbing it on the original panel), set group properties to use one hole as the reference point of the group. Move the group to 0,0. Then, you can again change the group properties to make the OTHER hole the reference point. Now, when you choose "move/rotate" the coordinates of the new group reference point will give you the distance between holes. It's kind of a process, but it works. It seems that almost everything in FPD is a "workaround". But it is pretty powerful software for FREE! I find that it is useful for making hole patterns for transfer to metal as well. Print in wiremode and print the reference points. Tape the printout to your workpiece and centerpunch the holes.
I would like to see them add some sort of "lock down" feature. I assume a real CAD program has a feature like this, but I don't know what it would be called. I have accidentally moved stuff just slightly and didn't notice it. Ouch.