Understood.
Re T-RackS version, the Leslie plug-in needs TR5 v5.1.0 or later (and, just for info, the Tape Machines, need 5.2.0 or later). Double-check that you have an appropriate version. Oddly, I'm on TR5 5.1.1 here but that is not listed in the "Past Releases" in my User Area. Anyway, rasie a Support Ticket and Technical Support will sort you out.
As for the dual Leslies (I just had a flashback to "duelling banjos
) that sounds like you were running them in parallel and combining their outputs.
I do not know Macs but I guess there is some way of virtually wiring the different programs together. I think that you might be able to load 2 Leslie FX in B-3X but they would be in series, one after the other. In AmpliTube there are 2 signal paths so you may be able to parallel the Leslies in there, using the "dry" audio from the B-3X.
To me the easiest way would be to use a DAW or plug-in chainer and route the audio in there as you wish.