Caulk, then set the toilet
Toilets should be caulked to the floor to prevent side-to-side movement that can break the wax seal (and to prevent splashes or overflows from puddling under the toilet and rotting the floor). DIYers often set the toilet and then apply a tiny bead of caulk along the outside edge. That doesn't always provide a good enough bond to the floor, and it leaves a prominent caulk line. There's an easier way to secure the toilet and provide a cleaner caulk line. Just follow this tip from master plumber Les Zell.
First set the toilet in place (without the wax ring) and square it up to the wall. Then make an outline of the toilet on the floor with masking tape. Remove the toilet and turn it on its side. Measure the depth and width of the gluing edge of the bowl. Next, move your caulk gun to the inset depth you just measured and apply caulk directly to the floor, maintaining the inset depth as you follow the tape. Install the wax ring and lower the toilet onto the flange. Stand on the toilet to compress the wax ring and ensure good contact with the caulk. Then use paper towels to clean up any caulk that oozed out.