Melissa, first of all, you must replace the wax ring every time. This is a $2 important task. You may find that the lugs are rusted and won't come off, sometimes you have to hax saw them off. So, a ring and lugs do come in a package together.
Here is the run down.
Shut off the water and if the valve has not been loosened in quite a while, gently turn the valve. use WD-40, (if Sparks agrees), to assist in the movement.
Drain the comode of all water. use a sponge or a wet vac.
Remove the water supply pipe from the comode, if old, consider replacing it with the new flex tube.
remove the lugs, saw if need be, then remove the comode and clean off all the old wax from the underneath of the comode and the floor pipe flange.
Stuff a old rag into the floor hole and don't let it fall down in the pipe, you will remove this at a later time.
Now get a putty scraper and remove all the old wax.
Set this aside if you can and continue the flooring. Melissa, if the flooring your adding is very high, the comode and the floor flange may have trouble connecting up. There is an extension that will need to be used if your adding too much space between the comode and the floor. You should be able to add 1/4 inch without any trouble.
When ready for re mounting the toilet, be sure and remove the rag. Then attach the flange bolts then attach the wax ring to the comode, there is a up and down side.
Set the lags in the flange and attach a straw to each lag bolt. This is my super assistant when re mounting the toilet. With the straw extensions, just line up each straw with the comode holes on the base and then gently lower the comode onto the flange which will automatically load up the flange bolts.
Attach the water line and use Teflon tape on all male joints.
Be sure and not ratched down on those flange bolts. run them down my hand then sit on the comode and waller a bit, then tighten one turn, then sit and waller again, then tighten one turn, do this until the comode is secure. Over tightening will only take a risk of cracking the comode base.
Your set after you caulk with 100% silicon around the base.