Steps order is used to specify how steps will be displayed in these places:

• Steps Tree in the right sidebar of process builder (1)
• Progress bar in sequential mode (2,  available in version 5.0 )

The step order is used just for visual comfort.

By default step order is corresponding to the sequence in which steps were added to the canvas, and may not correspond to the sequence in which steps will be proceeded. Order can be changed by user. To do this click "Set Order" button (3) at the steps tree:

You will go to Order Change mode (4) of Process Builder - all other parts of builder will be darkened:

Now any step (5) can be dragged with mouse to necessary places:

The predecessor of dragged step is highlighted with blue (6).
If branch, which dragged step belongs to, is ended with constraint, the last (constraint) step of this branch is highlighted with yellow (7).
Step can't be placed higher than it's predecessor. If try to do this, step will be outlined with red (8) and, if try to save order, proper warning will be shown (9):

If click "No", user will be returned to Change Order mode. If click "Yes", system will try to set order automatically by placing incorrect step directly after it's nearest predecessor (10):

After finishing order change, click "Apply" button (11) to save them or "Cancel" button (12) to discard changes:

If you try to cancel unsaved changes, system will show a confirmation popup: