if you swap to a 5spd (definate reccomendation with your proposed setup. due to cost and lifespan) you can run the evo ecu by itself. otherwise as run said you can run it as a dual ecu setupeither way i suggest getting a boomslang harness to simplify the install and make it reversable for that matter. i believe the conversion harness runs somehwere around $200 or so....there was also an issue with one wire that needed to be switched but if it wasnt corrected yet then there is info on which one it was
The conversion harness last time i checked is like 300 from boomslang but its worth it.
right ^ the harness im talking about is not listed but they will make it custom for 300. Email them -- the harness will be a Y harness in that you can cut wires that dont need to be and ur done pretty much... The primary end will connect to ur stock harness and split into two sets of harness connectors - one for evo and one for stock ecu.