The exhaust with the single CAT per side is for the early model V6 with engine code AHA.
The system with (2) CATs per side is the for the V6 engine code ATQ.
The ATQ engine had a fairly significant amount of changes compared to the AHA version. Most of them having to do with emissions.
Other changes having to do with oil delivery to the valve train on the cylinder head(s).
Incidentally AHA and ATQ heads can be swapped. AHA heads on an ATQ motor and ATQ heads on an AHA motor.
I don't know for certain because I've never actually done it, the ATQ engine will run with the AHA version exhaust, however I don't think it will pass emissions. I'm fairly certain the ATQ had tighter emissions tolerances.
The transmission being automatic or manual had nothing to with what exhaust was used.