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I would find out before you plug it into the bike and do anything because the FP3 marries to your vin # and you'll never be able to use it on another bike now return it once you take the plastic off the box it comes in
It will save whatever map that is already installed, and will flash the new map from Vance and Hines, then auto tune new map if you want to, yes it will work
Must the ecm have the stock flash to begin using the FP3 or will it work with a ecm that has a stage 1 flash?
Personally, I would have your dealer flash your bike back to stock.
You would would want the FP3 to have the stock settings to work off of and store into the memory, and there would be no chance of conflict between the two flashes.
It will save whatever map that is already installed, and will flash the new map from Vance and Hines, then auto tune new map if you want to, yes it will work
^^This.
Don't worry about dealer flash. It will have no impact using the flash from FP3.