I’ve usually found Audyssey very good.
I know you shouldn’t, but try try setting the mains to large (no subwoofer), run Audyssey again. (Usually picking large mains auto turns off the sub anyway)
After that turn on subwoofer and manually pick where you think the sub should come in and adjust the level. If you have big floor standers 30hz small ones 50hz bookshelves 80hz.
Cheers George