Well in theory you'd use the complete ECU and sensor set for the engine and transmission.
This means you'd need a AT engine + accompanying transmission.
This does give you the ability to run a 5AT transmission,
Although you'd need to find a way of integrating the shift linkage and other parts specific to the 5AT.
Paddle shifters would be quite a task though
6AT won't be cost effective.
In theory a 3.6/3.7 "hybrid" engine coupled to a 5AT sounds like a interesting NSX.
Term hybrid would refer to a 3.2 or 3.5 using 3.7 parts to create a 3.6L stroker or a full 3.7 engine.