I suggest starting out reading the entire help page in order to fully use this terrific tool.
If your dates are flexible, especially use the graph function! Torn whether or not to fly Saturday to Saturday or during the week to save some $$$. This is the easy way to look for it.
After you have chosen your flight segments, it will even show baggage fees.
At present it shows all major alliance airlines, it also includes Air Tran, Jet Blue and Spirit. It does not include pricing for Southwest, but when you expand your search it will show flight times for SW.