Combining home theater with two channel

I have been on this same journey. In fact, with Covid etc it has truly saved my life to have something that brings joy.   I switched from a HT mindset to a 2 channel mindset and it has made all the difference in the world.   The two mindsets are totally different. 
My only advice it to get as musical and revealing main speakers as you can afford.  And get a good pre-amp with home theater bypass. 

If you can get the stereo sound you want passing through your Marantz, then use identical amplification and the same brand of speakers for all channels. Certainly don't mix and match. The best test is to select stereo through all speakers. The least variation between channels the better. Levels and speaker distances must be set accurately. Room correction takes reflections into account, so these settings should be ignored. Rather than use a tape measure, get a laser measurement for each speaker from the primary listening position.

When doing room correction, cover your seating with wool blankets to stop measuring reflections from the seats.

Hi Peytoni,

I had the same experience as you while back and went the HT Bypass route.  Here are a couple of my discussion threads for reference:
https://forum.audiogon.com/discussions/optimizing-ht-setup-for-analog-where-to-begin
https://forum.audiogon.com/discussions/best-integrated-for-my-purposes-help-me-choose-1-of-3

I wanted to retain the mostly good HT performance, but didn't want to compromise any 2-channel listening.  I realized early on that my setup just wasn't optimum for the LS50s.  In the end, I went with a Parasound Hint6 - I couldn't be happier.  I was even able to sell my phono pre as the hint6 was better all around.  Just awesome.  There is a bit of inconvenience (for the family... not me :) when having to switch the hint6 into 'bypass' mode, but other than that, just a great setup.  Can also be solved with a smart remote.  

Anyway, no matter which way you go, a fully dedicated analog signal chain is where it's at! 

I prefer two separate systems.  The only commonality between my AV and audio systems are the main speakers,

When I want to switch from one to the other, I just take the speaker wires out of one amp and insert them in the other - I have a tube audio set up and a solid state video set up.

I have played music through the video sources but the sound from a mass market AV preamp, while quite decent (I also use a Marantz) is inferior to the stand alone audio set up.

You can’t get around the two system part. toasted my 25 year old Bose Lifestyle HT system. I’m about to go with a Nad t778 and pass through the additional back surround channels. I don’t really need the video switching though as the TV handles that fine. Started wondering about a tube amp as an old Sansui (smoked it) was so smooth. The money to power dual 15 JBLs with tubes is too much so I’m sticking with a Crown for the stereo. I personally just love the club sound levels and the JBL bass. I’m also getting addicted to the MQA (albeit less pure than analog , but convenient). Any insights into a sound only system that will process MQA and provide for HT pass through without the video? The Nad seems like one of few choices. MQA/ HT pass through and atmos are my hot points.