MSD DIS-2 with ECUFlash

[mechanix565]

So i just picked up a Black box ecu, COP setup and MSD DIS-2. Now i realize the MSD itself has two step and rev limiter functions built in but thats not why i bought it. I picked it up because i wanted a higher powered ignition system to run my individual coils because one i wanted to clean up my bay with individual coils and secondly because i wanted them to be as powerful if not more powerful than the stock coil setup. The actual wiring up of the MSD isnt the issue, my concern is after its installed how do i set it up so i can still control all the spark,timing, rev limits, two step etc from the ecu and not the msd, i dont want it to interfere with the settings im tuning into the ecu, how did everyone else set up their DIP switches? i do however want to use the brown wire on the MSD for an ignition kill switch but thats the only function other than the two ignition channels that i want to use it for.