If both sides speak it, RSTP. Because it's quicker to converge.
If you need background info any big switch manufacturer (Cisco, HP, Brocade) is going to have tons of free stuff to read on their websites on how spanning tree works, and what sets the different versions apart.
Specific answers require specific questions. When in doubt, post the output of "/ip address print detail", "/ip route print detail", "/interface print detail", "/ip firewall export", and an accurate network diagram.