Leave in original loom and ECU.

You need to get a wiring diagram (start studying a haynes manual!) and then splice into which bits you want the omex to run.

for example, fuel pump - injectors - fan - crank sensor (still needs to be read by the standard ecu!) - lambda sensor(s) - coilpack etc.

Cut the wire on the original loom at the hair brush connector and connect it to the specific omex wire which will be in the manual you get with the kit.

That way the omex controls the bits it needs to (engine) and the standard ecu still runs all the dials etc.