Best equipment to integrate subwoofers with desktop speakers?

I'd like to better integrate subs with my KEF LS50 speakers. I use them nearfield on my desktop. I use the setup a lot, so I'm willing to replace all the gear.

I usually drive them off a Schiit Yggdrasil/Ragnarok stack.  I've driven them with my floor standing set-up (Mytek Manhattan/Parasound JC5) and that's an improvement in every sonic way.   I sometimes add in subwoofers via XLR crossed at 80Hz which can improve the experience too (with SVS PB13 Ultra, they have some limited built in processing ability, but nothing changes to the signal the KEFs get which still run full range).  But the integration leaves something to be improved I think. 

I suspect this because I own a set of KEF LS50W too.  I prefer the passive LS50 setup to the LS50W (the imaging and vocals are just better).  But when I add in a subwoofer that changes.  The LS50W's built in processing options that can high pass the KEFs and send a sub out win over with the subwoofer integration.

I've considered a few other upgrade routes here:
-I am tempted to try out the Benchmark stack. DAC3, HPA4 pre, AHB2 x2 amps
-update the LS50 to the new META versions (haven't heard them yet, but interested)
-get a paired of sealed subs like SVS SB3000 (they're a lot smaller too which would help fit them behind the desk in front of me)

None of those fix the integration with sub issue though.  For that, I have been looking into:
-MiniDSP SHD. Would be DAC and DIRAC on 4 channels. So I could run room correction on the KEFs and the subs. I'd be stuck with digital volume control though.
-Any other preamp/processor options that have advanced subwoofer integration?  At least with the gear I've tried, most multichannel theater AVRs don't sound as good as a dedicated stereo pre.
-Should I just give up on the passive LS50 set and equipment stack and just get the new LS50 wireless II?  Seems to do everything I am looking for.  I just assumed I could build a better passive equipment stack on my own but when it comes to the subwoofer integration it seems to take out an option like the DAC3/HPA4...

Thanks