Stage numbers help you and the patient keep track of which model and aligner tray is which. Automatically placed on the molars (or the next tooth is available) of each arch is the current stage number. During treatment planning in the software, this number displays as 00. Once exported, the software generates the individual stage number. This raised number gets embossed on the aligner when vacuum formed.

The stage number repositions like an attachment. Clicking on the 00 brings up a dot and semi-circle. Clicking and dragging the dot allows you to move the number on the tooth or a different tooth. The semi-circle rotates the number. Clicking on anything else saves the position of the stage number.
By checking Separated Computation of Stages for Upper/Lower in Settings/Stage, the software generates the minimum required stages independently for each arch. This means the total stage count may differ between the upper and lower arches.
When this option is disabled, a unified stage count is applied to both arches, meaning they will always have the same total number of stages.

Separated stage computation and combined stage numbering

Combined stage computation and numbering
If the upper and lower arches have different total stage counts, and Use Separated Stage Numbering for Upper and Lower Arches is enabled in Settings/Stage, then their stages will be numbered differently.

Separated stage computation and numbering

Separated stage computation and combined stage numbering