Two Subwoofers Connection Advice

I don't think this applies in your case.  I think Velodyne is suggestion you create a monophonic sub signal.  that is, each sub combines L and R, hopefully improving room response.  It's not a bad idea.

In your case however, sinc the Marantz has dual sub outputs you can forego this and deal wiht it all in your bass management menu. 

Does the Marantz  label them sub 1 and sub 2 or left and right?  Can they be assigned Left and Right in the Marantz menu ?   That would be ideal, left to left and right to right.  

You could Google your module with that question if you don't have the manual.thats what I do and it's seems to find the answered on my denon and marantz avr.there getting alot better with the newer av 10 4 subs out with dsp for each in the room.enjoy the education and the music

I looked in your manuals, and this is what Marantz says about subs connections.

SW 1/2
(Subwoofer):

 

Place the SUBWOOFER at a convenient location near the front speakers. If you have two subwoofers, place them asymmetrically across the front of your room.

The manual feels like it is written for children :(

Either way, it looks like your sub outputs are mono.

Your subs have a built in crossover that lets you connect the amp to the sub, and use the high-pass filter to send signal to the speakers (stereo subs).

So you have a ton of flexibility on hook up. If you have speakers with drivers under 10", I would try to use stereo subs positioned near the speakers. If you have speakers with 10" or greater drivers, I would try to position the subs in 2 nulls in your room and run them mono using the sub output from the amp.
IMO, if you have a well treated room and the ability to properly place your speakers, you will get the best sound from stereo subs and no signal processing from the amp. Next best will be mono subs in the nulls with signal processing only on the subs or not at all.

-Josh

I have a Dayton Audio plate amp that has the same Y cable suggestion. I never tried it because I ran a single sub for 23 years using two ICs to LR inputs. The amp died and I replaced it 1 1/2 years ago and now it is malfunctioning anew  and have to send it back under warranty. The fun never stops.

I have since moved it to my bedroom and use the single LFE connection from my KEF LSX IIs thanks to excellent advice from a SVS tech who also owns KEF and was helping me set up my new SVS dual subs in my main system.

Long story short: I would heed Velodynes instruction until you contact them.