You should ALWAYS keep the bias switch set to match the type of tubes you are using. Don't change it unless you change to the other type of tubes. Failure to do so could possibly damage the amp.
EL34's have a bit more upper midrange character to them and a higher and tighter bass. EL34's also start to breakup sooner (i.e. less headroom) and do so more gradually. 6L6's have a bigger deeper sounding bass and a crisp sparkling high end. They tend to breakup later (i.e. more headroom) and a bit less gracefully. Some people say that EL34's sound more Marshall like while 6L6's sound more Fender and Boogie like. For many, EL34's are favored when more breakup or power tube distortion is desired, while 6L6's are favored when clarity and headroom are desired. Depeding on the amp and speakers, the difference can be subtle, so there really are no rules. The great thing about Boogies is you can try them both and use the one you like. As for output power, EL34's and 6L6's are pretty similar in that regard.