Separate Amp for AV receiver

Stereo (2-channel) is stereo, HT is HT, and never the twain shall meet.....I have three HT systems, two based on separates, one with an AVR. They are hardly ever used for music listening, maybe FM once in a while. I will have to admit that AIX discs in multi-channel format can sound pretty goodon a higher-level HT set-up, and all concert DVDs/Blu-Rays benefit from the format also. The trick there is that video is part of the mix on those discs, soit's akin to watching a movie (ever notice how music sound-tracks in movies usually sound pretty damn good?). The eye-candy enhances the audio portion and vice-versa.

Ok, lets take a look at ur HT speakers, what are you using ? Do you have subwoofer(s).
does the system lack slam ? If its HT ya gotta have slam, slam is where the money is Lol. Sounds like you have a nice 2ch system

Lets look a little closer at what its NOT doing for you, HT seems pretty straight forward, hook up all the speakers and bam its a HT, not always…..

Alright, I've decided upgrade the speakers for my HT first, they are twenty+/-. I started with a new subwoofer. Just installed a new REL 7X. I also have a REL S/3 SHO for my two channel system, along with my 803 D3s, so I would like to go with both subs by connecting my Denon AVR4300 direct with the REL 7X, and using the "Longbow" REL wireless connection to the S/3 SHO. I can't seem to get them to pair although I've tried multiple times.
Anyhow the sound is much improved with the new 7X. My front speakers for my HT are NHT 2.5i, very efficient speaker. The rears are ceiling mounted Klipsch, don't know the mod. #, but they have three speakers facing down, front and rear. The upper clg. mtd. fronts are Boston Acoustics with front facing and rear facing speakers. The Center channel is Martin Logan Motion 50XT.
I think I'll keep the center channel, it's only a couple of years old, but change out the upper rears, and upper fronts first. 
Please advise, what do you think.
Thank you

You have quite an array of manufacturers there. The NHT’s show a 86db sensitivity which is not very efficient.
klipsch are usually in the hi 90’s which means they require more current than Klipsch.
the ML 50xt is rated at 94bd thats more sensitive requiring a little less juice.

i dont know what cgl.mtd means.

with this mismatch system im seeing why you are not happy. They all have a different signature. Power wise a nice 7ch 200watt per should do you well, its not going to sound bad, it just not gonna sound balanced.

if you research mastering suites for dolby atmos you will notice rooms with all the same speakers