Fmf fuel programmer install question

I've finally bitten the bullet and bought all the common mods for the 09 wr250r. I've got the q4, megabomb, and fmf programmer installed. The question I have is this: when I turn the key to start, I don't hear the injectors prime like I used to. When installing the programmer, I disconnected the factor injection connector and replaced it with the one from FMF, there is a second connector on the FMF wiring which I attached the factory injection connector to. Is this correct? The FMF instructions don't exactly say. I haven't tried to start it as I'm waiting 24 hours for my high temp silicone sealant to cure (painful.....).

Yes, that's correct,
The programmer is put in between the original connection from the wire harness and throttle body.

Don't forget to connect it to the battery...