The PBn codes simply rearrange your build orders. A starbase with one of these friendly codes jumps the queue and has its build order fulfilled prior to any of your bases without a build order override, and prior to any of your bases with a build order override using a higher number.
Let's assume you have three build orders:
Base #100 Priority 10000 Base #200 Priority 9000 Base #300 Priority 5000
Over several turns, the priority values will increase but it will still be the case that the ship at base #100 will be built first, followed by the ship at base #200, and finally the ship at base #300. Now, if the friendly code at planet #300 is set to PB1, the build queue will appear as follows (assuming priorities haven't increased):
Base #300 Priority 10000 (using PB1) Base #100 Priority 9000 Base #200 Priority 5000
Note how base #300 has jumped to the top of the queue and all other bases have been "pushed down" in order. Priorities haven't changed, however. In a real game, the priority numbers will increase as usual, but what is important to note is that build order overrides do not affect your priorities, nor do priorities have any effect on build order overrides. In other words, you cannot change the order of ship builds relative to other players, you can only change the order relative to your own bases.
Once a build order has been reordered using an override it is not necessary to maintain this special friendly code on subsequent turns. The new ordering is maintained in the build queue until a different override code possibly changes it again.
The override numbers 1 through 9 are used to set a relative order, where PB1 indicates the build order to be fulfilled first. Override codes need not be used sequentially. Two bases can be set to a specific order using PB1 and PB2, or PB1 and PB5, or PB8 and PB9, for example. Bases without override codes maintain their relative order but will always appear later in the build queue than any base with an override code.