You put the engine on as per specs.

You ( Normally, but with a few exceptions ) DO NOT move the engine from the recommended.

Most planes either come pre-drilled or have a sort of cross hair on the firewall which represents where the center of the BASE of the mount is supposed to go.

Most mounts and engines come with guide lines that help you get everything lined up.

What Tower sells is a C.G. tool and a "hole locator".

The hole locator is used to find where to DRILL on the mount with the engine at the specified location.

All you do with it is scribe a mark where you will subsequently drill.

This is a bit harder than it looks because the engine gets in the way, and othersie you would tend to offset the hole too much if you used, say a pen, or a drill bit.

The C.G. tool is used to adjust the weight of the components in the plane to get the plane to balance at the recommended location.

It's not the other way around.

Once you've flown the plane as per spec you can adjust the C.G. to your liking, but the engine tends to stay put.