Originally Posted by dontcallitarex
Leave it how it is. The ECU will adjust the map to the intake.
HOWEVER, the details on the map reiterate like 5 times that you use ONLY THE STOCK AIRBOX. Not saying your motor is going to explode, but your AFRs might be a little screwy and you might throw CELs occasionally. Cobb says that you can use their own SR with the map without issue, though.
You can also use the Cobb intake. quoted from cobbtuning.com : "The COBB Tuning SF Intake system is compatible with Stage 1 and Stage 2 OTS (off the shelf mapping) provided for our AccessPORT ecu tuning device."