I think this is what should happen but maybe it's a setting I'm missing. After a MANUAL autofocus on say an Ha filter.....is the position supposed to be auto imported into the filter setup Focus Pt?
It is not. Running AF outside a sequence will only adjust the current position of the focuser and will not alter any settings. You can use the controls in the control panel focus tab to push the current position into the AF position settings for that filter.
Ah, so if you run Autofocus as part of a sequence, the "new position" will update and this update is good for any NEW sequences?
No, sorry, I only used that terminology because your OP referred to it. AF, in no way, at any time will adjust sequence parameters, only the current position of the focuser.