Go to the Battle Control Window (F8) There is a list of each task group there, and as you go into the tree you will be able to get to an individual ship. Set up one ship for each class with the basics of which fire control for which weapon/ecm ect. Also make sure to put all weapons on a point defense setting. Then go over to the far right where there is a set of buttons labeled Coppy Assign. Hit the one for your race. This will copy the basic setup to all of your ships in that class. When you get into combat you will need to change things around, but this set things up for you.
A couple of hints. Make sure you specify which type of missile to load for each launcher. Set all beam weapons on final point defense unless there is a good reason not to. This will help if a fleet is shot at by suprise. I would also assign your best eccm to the best point defense setup on the ship. You will end up changing it in combat, but it can help a lot against enemy missiles with ecm.
Brian