If their target is a station, their target continues to be the station after they've disabled it.
If it was a ship, though, and the ship got destroyed (even if it was a friendly ship), their new target would be whatever target that ship had (so if it was a transport going to a planet, your ships would go to that planet after the transport was destroyed).
And there isn't a way to set up multiple targets for them to go at in succession. The method used for most people that I know of for directing fleets is just setting them all to follow your ship, and going where you want them to go when you want them to go there.
------------------
"Social lives are for the weak."