Here is one work around you can use. Below I have renamed your original zones 1, 2, 3 to zones 2, 3, 4, you will see why.
1. Set up that pump station as a ‘master zone’ — in Edit Options -> Configure Master, set the appropriate zone as the master zone. For example, if your pump is installed on zone 8, set zone 8 as master.
2. Move your original zones 1 and 2 wires to ports 2 and 3, making zone 1 available as a ‘dummy’ zone. This is used solely to trigger master zone to run (in the beginning like you wanted), and will NOT activate any valve.
3. Configure zones 2 and 3 to NOT ‘Use Master 1’. Specifically, in their zone attribute dialog, uncheck ‘Use Master 1’.
4. Create a program, set zone 1 to be whatever amount of time you need to fill the tank, then the other three zones with their desired amount of water time. This way, zone 1 (dummy zone) will start first (will not activate any valve because that zone has no wire connected to it) — it will activate the master / pump, and fill the tank. Then zone 2 and 3 will run (these two will NOT activate master because their ‘Use Master 1’ has been unchecked). Finally, zone 4 will run and active the master.