nope it wont matter if your mods are cobb or not. for cobbs access port off the shelt maps its best to stay with what they tuned the car to have on it. like stage one is ment for a completely stock car, and stage two is ment for a car with a high flow catted downpipe and exhaust. if you go much further then that you can use the cobb access port racetuner software and tune custom maps. if you a 06 and up wrx or an sti you can even go with speed density with the custom maps if you choose. its a handy thing to have if you dont want to go standalone ecu.