http://monerotoruzizulg5ttgat2emf4d6fbmiea25detrmmy7erypseyteyd.onion/resources/user-guides/multisig-messaging-system.html
The MMS does not care about subaddresses and accounts; whatever address you use for sending (and receiving) transactions, the MMS only cares about the data that the particular event creates, about the right moment to process that and about sending it to the right recipient(s). If you don't like your transaction data to become part of the .mms file in the form of stored message content, you can use the normal transfer command, but then it's of course your problem to send...