Plumbers putty is not used for setting toilets.
The process is this:
The toilet flange lever should be no higher than 1/4" above nor 1/2" below floor level. An extra thick bowl wax or a second on without a plastic taper flow gasket can be added to get sufficient material for a good seal.
Once the toilet is set on the bowl wax and the nuts on the closet bolts are moderately snug. Bolt should be secured to the closet flange firmly with a washer and nut. All hardware must me non-ferrous.
If the floor is not perfectly level you'll have a little extra work to dl. Shims will be needs (soft plastic wedges available at the plumbing warehouse) to push under the bowl rim to get it and tank level in all directions. The bowl nuts are then snugged down. The wedges are then trimmed with a sharp blade. To get the best seal between the bowl and floor a sanded caulk is the best choice. These caulks (water soluble) are available at any good floor tile supplier and can be had in a myriad of colors to suit the floor color, grout lines or toilet ceramic as the case may be.
Been at it for 36 years now. Do it right, do it once, do it wrong, do it at least three times. It why plumbers get their wage. I have to fix if for free for a year if anything fails.
Merry Christmas, Rich