To adjust Shimano Altus gears, first set the limit screws by adjusting the high (H) and low (L) limit screws to ensure the derailleur does not overshift the chain. Next, adjust the B-tension screw to align the derailleur properly with the cassette. Finally, fine-tune the indexing by using the barrel adjuster on the derailleur or shifter to adjust the cable tension, ensuring smooth shifting between gears.