Hi Lee,
From my understanding of Alpha systems, they can plug directly into NCE systems and then the output from the NCE can be split into track and accessories. i.e. It does not have to be a combined bus as you seem to think it must be ?
It is the Digital IP that has the capability of being connected directly to the DCC bus and only one other wire powering the frog, negating the need for auxiliary switching of the track power to the frog.
Yet - it can also be wired from an accessory bus and track power switched through the auxiliary switch - as is the normal case for Tortoises and solenoids and servos with external micro switches
I always find pictures speak a thousand words when problem solving ... do you have any photos of the layout wiring and maybe the power of the forum can help with this ??