I assume this is not a lambic or gueze style beer? When you go to secondary it you will want to transfer to a larger vessel and dump your cherry puree or what ever you have before the beer and put on top... I know some people also try when racking to get some of the yeast from the bottom and also place some in there as a buffer... I'm not 100% sure on this though...
The beer after primary should be close to finishing gravity but not completely... once you rack you ontop of the sour cherrys you will see a jump in activity... I would leave it on the cherrys for at least 2 weeks and then rack off the cherrys again to a bright tank or another carboy so all the sediment drops out and clears.