To begin, Allisons are available with an SAE 3 bellhousing which will bolt directly up to any 4 or 6BT Cummins.
But the cool part is that the new generation Allisons now have a single on-board computer that allows them to talk to an all mechanical engine via nothing more than a TPS (throttle position sensor). This is a really huge deal since the earlier models were mind-bogglingly complicated to hook up. I've talked to guys who've spent three years trying to get all the programming & wire harness issues worked out and are still having problems. With the new Allisons, it is pretty much plug & play. The TCM (transmission Control Module) does need to be flashed (they come clean from the factory) but there are already folks out there who can flash them by mail or you can take the unit to any authorized Allison shop and they can do it.
All of this means you can now bolt up a state-of-the-art, six-speed, double overdrive automatic transmission to any early, all mechanical Cummins 4 or 6BT engine.