Hi,
The main difference as I see it is in the SWAT setup phase: watershed delineation,etc.
Both of them follow the same procedure only in a slightly different way. For example: QSWAT uses TauDem for deliniation, AcrSWAT uses ArcHydro delineation procedures.Which is better? There is no right answer to it.
Next, the subwatershed definition: ArcSWAT uses your inlet/outlets to define the subbasins, whereas QSWAT uses a threshold-based approach.Again, which is better? Depends on your watershed and what are you trying to achieve.
After the delineation and hru definition - they are the same, because the both use SWAT Editor.
Best,
Natalja