Your monitors do not need to be in the same resolution, but you might be happier with the visuals if they ARE in the same resolution.

For dual monitors I highly recommend using the new method I've been demonstrating this year with Video Feeds.
playing 2 EVE ships on dual monitors: http://www.dual-boxing.com/showthread.php?t=41982
playing 5 WoWs on dual monitors: http://isboxer.com/forum/viewtopic.php?f=35&t=1222

With this method, all of your windows are the same size because they're all on the same screen and stacked in the same position. Full visibility is provided by fully interactive video feeds (yep, I can click on anything you see, or i can move the mouse over it and type, etc) and you minimize your wasted space on the second monitor by making the important things bigger!