The bass keyboard is less flexible than the treble. Work out your bellows direction based on the needs of the left hand first, and let that dictate right hand fingering.
If you're playing chords in the left hand, you'll find that in many keys (e.g. F, C, G, D, A, E), the tonic and dominant work out easily in opposite bellows directions; of course this was done on purpose for folk music.
The bellows and air valve are critical. Learn to anticipate bellows direction changes and as you approach a change, slowly leak air through the valve while playing so the bellows is positioned comfortably for the next passage.
Depending on your style, some of this may not apply; for example, Argentine Tango players play their bandoneóns almost entirely on the draw of the bellows and use the air valve to push out a big puff of air between passages.