Your first question makes no sense to me. When you set a toilet, you are merely sealing it against the flange using a wax ring. No caulk is necessary.
You can stop the bolts from moving around as you tighten them by using a locking washer or a nut to snug the bolts up firm against the top of the flange (thus effectively locking them in place).
The more expensive toilet floor bolt kits come with this additional hardware.