Stereo Preamp suggestion

I was in exactly the same situation a couple of years ago and the solution is easy and extremely satisfying sonically.    
Adding a preamp with HT bypass will be a significant improvement, as it removes the Marantz's preamp from the system. Although you do not provide any source information, I assume you use either vinyl, CD or digital of some sort, so all 2-channel will run through the preamp. If you were to buy the Parasound Halo P6 it would solve a lot of what you are looking for. It not only has HT bypass and dual sub outs, it also has a set of additional sub outs with variable low pass filter and a variable high pass filter for the main outs. 

Mcintosh has “passthru” on many of their preamp‘s. I’ve owned the C1000 and the C8. Both of work flawlessly

A budget number would be helpful.  I used a Modwright LS100 until recently and have since upgraded to a Herron VTSP-360 Reference.  Both have HTBP. 

My subs are active for both stereo listening and home theater.  Many preamps have more than one set of outputs.  You will give up the subwoofer correction from your AVR, but if you run enough subs (I have 4, 5 for HT), it won't matter.

I’m not 100% positive but I think for what you are trying to do only the parasound p6 or anthem str will actually do what you want. I believe they have HT bypass for the RL speakers as well as subwoofers. I had the P5 not the P6 and found it really to be not much better than the marantz prepro I used for HT in regards to 2 channel music. The anthem STR is probably my vote out of the 4 because it has the features you want and will sound better than the parasound but it is over double the price.

I have to agree with last two posters. The Parasound P6 is just want you want to integrate 2.1 with 5.x from AVR. I had the P5 and now P7. The subwoofer can work with both.  I use Roon and DSP for 2.1 and anthem avm60 arc for theater. Best of both.