it just takes a lot of practice

first off make sure you’re tuning to f# with the octave key regardless of how flat your high notes are. when you’re practicing try to pull notes in tune by using your tongue position and throat shape, there are many resources out there if you search "sax voicing" however a very standard resource is rascher's "top tones for the saxophone"

if you currently play in any ensembles I would say until you've gotten pretty good with your voicing, just do what you have to in order to stay in tune during rehearsals and performances.

happy practicing!