We have a few customers that run two S12EQ or Two S10EQ.
I recommend renaming the existing subwoofer in the app, before setting up the second sub.
You rename the speaker in the app in the Discover & Connect menu. Swipe the active subwoofer to the left and you should see configure. In the configure, you should be able to rename the subwoofer. If you using the android you may need to update the passcode at the same time. Once renamed, you should be able to plug in the new subwoofer and set it up.
The Discover & Connect is where you would switch back and forth between the two subwoofers. I recommend running the Auto Eq on both subwoofers and then re-running the auto eq on the receiver.
If you have any questions let me know.