Setting the the HP on the amp AND running the passive crossover will have a negative effect on the tweeter... it will change the crossover points set by both and give you and indeterminable crossover freq. The amps HP filter can only be set as high as 250hz per the manual, so its pretty much useless in your case... I would set it to AP on the amp and let the passive RTS crossovers do their job.
As for the mids, as nice as the 4000NEX unit is (I actually am running the same headunit) it can't give you a crossover LP freq high enough (around 3.5khz or so to match up with RTS HP crossover point) to do a "poor man's" bandpass, so you will need an external crossover... Audiopipe makes an inexpensive one, as well as Lanzar (the x5 vibe, that Ive used in the past) and for a little more there is the Mclaren MLX-1000 that will give you 2 BP outputs if your system needs change down the road and you want to run a 3 way active front...
Once you put in an external crossover, I would just do all the crossover duties with it (tweeter, mids and subs..) just to make it all the from the same source... No passive crossovers (RTS's), set headunit to no filters (HPF, LPF off), set all amps to AP/Full and set the crossover appropriately...