I have a 97se 5spd. I was thinking about getting a modified ECU (JWT) pretty soon. The NOS kit a little later after I recooperate from the damage the JWT ECU does to my wallet. If I tell them to put the nitrous program on the ECU before I install a NOS kit will that retard my performance? Is that good for the car?

 

they will install a nitrous daughter board. I am sure it costs more, but from what I know it will retard your timing only while on the bottle. The rest of the time you should get the full benifit of the ECU upgrade.

 

Plurco is right, it works on a switch. You can switch for N/A performance (increasing timing, air/fuel, etc) or nitrous performance (preventing detonation). It costs about $300 more than a normal JWT ECU if I remember correctly, and will help your times under both circumstances.
-Cyrus