Yea, it would be easier for you to have them wire it up in a dual ECU format. You're auto right? Then dual ECU is a good solution.
I have a question though, why can't the shop flash it for you? If they can't flash it, then they aren't going to be able to tune it for you. Thats how you tune with a dual ecu setup. You read/flash on the EVO ECU which controls the engine.
Also, if you're auto, the EVO ROM won't work in your ECU, it won't control the transmission.