Valet 554r 04 Ram Newbie Help

I'm a competent mechanic and better than average with electrical repairs but this will be my first Alarm/RS install on my own truck.  I bought the system and I got the 555 key bypass, and also a Seperate door lock relay module.  From reading the directions and this website for the past couple of weeks I Think I have a pretty decent grasp of what goes where.   My question, is there a way to use the 5554r system to control the factory alarm & keyless entry so I don't have to tie into any door lock wiring at all?  I see that the DEI system talks about factory arm/disarm wires but I'm confused about how that would work.  I also bought the Bitwriter because I plan on installing the same system in my wifes 05 Equinox if this will make anything easier.  Thanks in advance for any help.