With Unifit equipped toilets, I shim at the back, making sure the front of the bowl is in contact with the floor.
You may need to loosen the back bolts before the shims are placed.
When the bowl is stable, then you can tighten down the bolts.
The front of the bowl can then be caulked.
You don't want these bowls to rock back and forth.
Plumbers putty is not used for shimming.