I've always used my right thumb, it's home position is usually 3. i have a pretty weird playstyle because I spent a lot of time playing beatmania exclusively one handed before I ever played IIDX at all. My left hand usually only takes the 1 key and sometimes the 2, but I've changed more and more the longer I've played. You just kind of move your hands however you need to to play the song.
I should try working my left thumb in more but it always feels really crowded and awkward when I do.
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