I do not think you can run the SK1 through the ipad app for its leslie effect, unless someone knows if that is possible. I think they have a vst version of the leslie only. You would just run the B3X directly through its internal leslie and can use the sk1 just as a controller. For precautionary reasons in case the ipad or app froze since it was the first time I used it, I also ran audio from the sk1 at a much lower volume (think layered effect) - all drawbars, chorus, percussion, leslie are auto-mapped. The drawbars are fairly similar so it does not sound like some midi layer, but when you kick in the leslie is where you really hear the difference over the standard internal SK1 leslie.
These guys did a real good video for the vst version, more in the gospel vein, but you can hear it here: