I know exactly what you mean, I used to find this a right PITA because when you produce a G Code you lose the original drawing, in my case a DXF file.

To fix it I rewrote my cutting software to read in the DXF and every circle shows on screen with a little red rectangle in the middle.

Right button the rectangle and it sets machine co-ordinates to the circle centre, left button it and it moves the tool to the circle centre.

I can also click left or right anywhere on the drawing, which is handy to make sure the cut doesn't overhang the billet.

What I do is drill some holes for locating bolts then clear the mill bed of everything.

I have a bunch of 3/4" thick mounts which have a T slot fixing and an offset stud with a female thread. I made 4 of each in M3 M4 M5 M6 and M8.

I locate the mounts by left buttoning rectangles, lock them in place, replace the billet and bolt it down.

If I have clear space and remembered to add a spare circle to the drawing, I pop in a centre hole so I can relocate if I lose position.

Lots of typing but I would not be without it.

When I am not machining the outside of the billet and need to align metal to the bed, I use the 10mm square tool steel bar I inset a few mm deep at the back of the bed. I cut the pocket for it with the mill so I know it is dead square. It has a splash guard holder on the top.

If trying to align to a centre scratch I start light with a centre drill and go progressively deeper with each attempt to erase the old mark. Really need a sensitive drill handle and a pendant for that.