Can I wait to refill the ink tanks until they are completely empty?

No. The ink level must remain above 2.8 inches (70 mm) from the base of the ink tank at all times. If the ink level falls below 2.8 inches (70 mm), replace the ink chip unit and refill the ink as soon as possible. Failing to do so may allow air into the ink system and affect your printouts.
Related tasks
Replacing the Chip Unit and Refilling Ink