My Sonus Faber Amatis have weak bass even though I'm running ML 536s--800 w/ch into 4 ohms

Stupid question - is your judgement of bass based on critical listening with the chair in the middle or is bass lacking in general. It’s possible you’re sitting in a bass null.
Or the setup is just not optimal. Can you post pics in the virtual system section of your profile?

Some beautiful speakers you have there - congrats! 

I will pile on that the SF are just not pressurizing the room, which when you put it all together from your description, is quite large.  Try walking around the room and stopping here and there.  You should find places where you can actually 'feel' more bass peaks.  I know my pretty large (long) basement room has much more bass (too much) along the sides and towards the back.  Fortunately, the listening position gives me a good combo of punch and depth.  If you don't feel the bass substantially more in certain places then I suspect it's a pressurization issue.  

Sounds like you've tried moving them around as much as possible with little effect.  Just leave the subs on and do your best to optimize everything.  Then relax and enjoy your great setup!

That Classe' has a high pass setting when using a sub. Are you certain you are sending full range to the speakers when the KEF subs are not used?

Page 28 of the Classe' manual.

Good luck!

@torke : I have recently tried the Amatis’ (somewhat) smaller siblings, the Serafino, at home for almost two weeks. I returned them in the end because of what I perceived as a very colored sound. The highs and upper mids, while truly beautiful in their own right, were much too emphasized. The bass didn’t lack extension, there just seemed to be comparatively too little of it (along with the weak lower midrange). I have also heard a pair of Amatis for a few hours at a friend’s house, cramped in a very very small room right against the wall (so bass was plentiful there) and as far as I could tell the same basic tilted up sound signature was there as well. I’m a lover of classical and jazz music just as you and, for my ears, these new SF speakers didn’t quite cut it in terms of timbre naturalness, the BBC speakers I’ve owned (Spendor, Harbeth, Graham) being better in this regard (but also lower in resolution and with less extension both ways, not exactly in the same class, unfortunately - to be expected given the price difference). This shouldn’t be construed as me saying they are bad speakers, they do some fabulous things like those sweet and silky highs and the "musicality" and I’ve been almost obsessed with them for a few years but, on closer inspection, natural sounding they are not...

@torke 

I believe you nailed it that it is simply your room.  That is tough for any of us to diagnose and advise upon simply by commenting in a thread.  I have Wilson Sophia 1 that have a lot of bass that is clean and deep in my room.  When I had some Egglestonworks Vigintis and Wilson Alexia 1 they both were very weak with significantly less bottom end compared to the Sophias.  On paper this makes zero sense.  I visited a guy and listened to his Wilson Sasha DAW with ample amplification and the sound was the most boring sound I have ever heard from a hifi system.  It was shocking how little bass and realism the system had.  I totally understand the psychology of feeling that you should not need subs but maybe you do.  I am sure when you have them properly paired with your SF speakers the SF will provide the remainder of the spectrum beautifully so let them work together and enjoy the end result.