The "321" EQ mode is the most rudimentary automatic EQ mode that the SMS-1 offers, and it's not one that I'd recommend even bothering with. It sends signals straight to the sub, so it doesn't involve the receiver's bass management and doesn't allow for any adjustment of sub level relative to front channel level.
You don't need to. The two auto EQ's are separate processes. The auto EQ that is available while in the main setup menu (the "12345" mode) sends tones through the receiver, but it still doesn't offer the level of adjustment afforded by the manual mode.
Here's the deal with running the SMS-1's output into the receiver. The SMS-1 generates a test tone, and the test tone has to be piped through the receiver. The receiver then feeds it through its internal bass management and divides it between the mains and the sub. This lets you equalize channel levels between mains and sub as well as adjust the subwoofer channel EQ's. Without the connection to the receiver, the only way to get a test tone to the sub is the Self EQ (the "321" automatic EQ system).