Regarding the second part of your question about sub integration: Your mileage may vary, but unfortunately, I think what you outline in your question would either be suboptimal or not work at all. Here are the issues you might encounter:
- If you manage to convert the SPDIF signal coming from the second speaker to analog via a DAC, you will get two separate channels, one R and one L. Hence, your subwoofer needs to have separate R+L RCA inputs (which it then sums up internally). Not all cheap subs have this, as far as I know.
- Volume control will only work if you use a source that digitally attenuates the SPDIF signal that you feed to your speakers. I think it will not work if you use the MA-1 kit to control volume directly within the speakers, as this way, only the speakers' volume but not the sub's volume would be affected.
- Your speakers are not high-passed and run full range. That makes integrating the subwoofer tricky, as you have to figure out at which frequency and with which slope they roll off. (You may be able to use the MA-1 kit to force them to roll off at a specific frequency with a predefined slope, but I don’t know whether that’s possible.)
- If your sub does not have a built-in DSP, the slope of its low-pass filter will probably not match the slope of the speakers' natural roll-off.
- Even if you can approximately match the slopes of the speakers' and the sub's frequency roll-offs at the crossover, you still have to level-match and phase-align the subwoofer manually.
- Finally, if the subwoofer has no DSP, you cannot room-correct it. This could mess up the whole sound.
- In sum, I think the overall sound quality could actually be worse compared to using your MA-1-calibrated speakers alone.
If you have Neumann speakers and use the MA-1 kit to room-correct them, the obvious way to add a subwoofer is to buy the pricey but competent KH 750.
Alternatively, you could integrate a relatively cheap hifi sub with a minidsp Flex digital, which can act as an active crossover, volume control, and DSP for the sub. That is, you could feed the SPDIF signal to the miniDSP and use it to set the crossover and time-align & room-correct the sub. More specifically, you would output i) a high-passed SPDIF signal to the speakers (which are room-corrected via MA-1) and ii) a R&L-summed, low-passed, and room-corrected SPDIF signal to a cheap DAC connected to your hifi sub. In the miniDSP, you could time-align the two signals, i) and ii), to properly integrate the subwoofer. As all of this cannot be done by ear, you would also need to buy a UMIK-1 to take measurements and use REW to determine the time-alignment and the room correction filters for the sub.
(All of the above could probably also be achieved with a PC & a digital audio interface (such as the Motu 8D). This would give you even more flexibility than the miniDSP Flex digital but has a steeper learning curve.)
Regarding the first part of your question: Unfortunately, I don't know whether the filters set by the MA-1 kit are stored in the speakers and will still work when you disconnect the kit and use digital instead of analog input. I guess so, but I am really not sure.