Once you have chosen your side you need to do your initial setup. Mostly this involves assigned your starting ships to worlds within your Pocket Empire. First you select one or more ships from the Ship Panel. You can select a world from the Star Panel. Click "Set" and the ships will be assigned. Alternatively you can drag ships from the ship panel and drop them on the star panel to assign them. When a ship has been assigned, the "to do" arrow will be filled in.
In some scenarios you are allowed to reconfigure your fleet before the game starts. To exchange ships, first select one or more ships and click "Scrap". This destroys the ships and adds their cost to your resources value. You can then click the "Build" button. This will bring up the Ship Building Dialog from which you can design new ships.
At any point you can click "Reset" to unassign all ships. Note, any custom ships are retained. This only resets their deployments.
When you have assigned all ships you can click the "Done" button to move on to the first turn.