OK let me explain with some wiring diagrams. These are actual diagrams of the equipment you own.
OPTION 1
Do what Genelec tells you to do. Motu Ultralite Mk5 (Ch 1, 2) --> Genelec 7040A subwoofer (L, R inputs) --> Genelec 8030C speakers.
Advantage of doing this: you will be using the 7040A's built-in crossover at 85Hz and high passing your speakers. This frees your speakers up from bass duties - usually distortion is improved, you get more flexibility with subwoofer placement, and so on.
Disadvantage:
turning off your subwoofer means no signal goes to your speakers. None of the previous suggestions - smart plugs, crawling under the floor to unplug the sub, etc. will work! If your sub is off, that's it. No music.
OPTION 2
Motu Ultralite Mk5 (Ch 1, 2) --> Genelec 7040A subwoofer (L, R)
Motu Ultralite Mk5 (Ch 3, 4) --> Genelec 8030C speakers (L, R)
Advantage of doing this:
- You can control your subwoofer independently of your speakers. Including muting it with Motu's mixer.
- If you use third party DSP, you can potentially achieve far better results than the rather crude high pass built in to Genelec's sub.
Disadvantage: If you want to use Genelec's GLM, you can not connect your system this way. More importantly, this option leaves no high pass for the speakers, so you do not get the full benefit of the subwoofer. You can opt to leave it (some people do), or you can DIY your own DSP with third party software. But DIY DSP is not easy.
OPTION 3
This is essentially the same as option 2, but this time the PC sums L and R into mono instead of letting the Genelec subwoofer do it. If you use Roon or JRiver, those already have built-in convolvers, although setting them up takes a bit of explanation. You could use third party convolvers like CamillaDSP (free) or paid convolvers like Hang Loose Convolver. I believe Foobar 2000 can also do this but I am far from a Foobar expert. In fact I wouldn't describe myself as a computer audio expert at all.
This is the configuration I am using, although I own 2 subwoofers and my speakers are fully active - so I use all 8 channels on my RME.