Do No Harm ... well the least harm anyway

It looks like there is a thru output so you can do a little A=100hz or B=thru= 20 hz. 

please make sure you turn your equipment off before you connect/ disconnect cables. 

If those speakers have “Thumpy” bass it’s either your room or most likely the position of the speakers.  Probably they’re too close to the front and side walls.  
Before you try surgery or software, I’d start with pulling them three feet from the front wall.  That’s three feet from the back of speakers.

All the best.

+1 @soix

With speakers going down to 26Hz (not including the room), I would think you would start with the subs crossing over around 30Hz and play with the gain first, and then adjust +/- 5Hz and dial in from there. 

IMO phase should be set to zero as your subs are next to your speakers. 

And definitely play around with speaker placement. It is amazing how much a few inches in distance in any direction and 1/2 inch more or less toe in (or none) makes.

Lastly, what connection method are you using? I don't know what Velodyne recommends for 2 channel but my experience with REL is high-level from the speaker taps works best.

My 2 subs are VINO (Velodyne in name only) because, being Velodyne, they have both broken. Tired of repairing them, I bypassed the electronics and ran wires to just the drivers. So now they are 15" passive subs. I use a Crown 2500 for the lowpass (55Hz) and all is working fine. When I said "thumpy bass" I meant that in a good way. Like the sound from a kick drum, those frequencies are best suited to subs, not to a full-range driver. My preamp has 2 outputs (XLR and RCA) so the XLR goes to my Benchmark amp and the RCA to the Crown. Interestingly I have found that hooking the subs out of phase produces more bass than in phase. Even though the subs are close to the main speakers. Perhaps the Crown amp inverts phase, but I don't know. Everything sounds pretty nice right now, but as a hobbyist, I am always thinking of something to change.

The only way to do it with least detriment is digitally. And even then you’ll need to carefully choose the product.