To set a rally point:
click on the icon in the top-left of the UIF (near the esponoige icon) at the bottom of the screen. Click on a parsec to place it, then select one of the options:
Set "fleet" option to make ships form into a fleet when they reach (I find this useful for building small ships to create a fighter fleet near a military starbase; eliminates a lot of same select/send/formfleet mouseclicks). Ships also form into a fleet when you send them there manually. Set "none" option for ships to simply go there.
To set rally point destination for ships:
Planets: click on the icon in the small window containing a picture of the planet then select the rally point, and the icon changes colour. To cancel this you have to click again and select "none" rally point (a few times have I changed a planet's ship production and ended up with transports hidden in fleets of constructors). This is good for setting destinations for many constructors from many planets to resources, or collecting spares into a fleet.
When the rally point is moved, all the ships divert to the new destination; a quick way of diverting your resource-bound constructors if you suddenly go to war.
To delete a rally point:
Click on it then select the "disband" option. Ships with that destination stop travelling and wait for more orders.
To send a ship there manually:
Select the ship then select the rally option (I use the shortcut key "T", I forget where the icon is). Select the rally point, the ship will go there.
The "planet governors" screen has options for changing multiple rally points, but I haven't looked into it much.
That is not a complete description of the GalCivII rally points.
