MTEnG- Since you have the EMI....you either have to put the key in the transponder ( wouldnt recommend it ) or use a DEI module I think its the 555u but that one doesnt require you to cut your key and leave it in there.

I have an autopage alarm on my car and am using a DEI module to bypass my EMI.
I didnt have to cut my key or anything since the module memories the codes or something to enable you to remote start your car.
I might have the documentation at my house so if I do I will scan my wiring diagram cause it shows what connects to what.