Firstly you can only make a maximum of 3 ISDs when they are available. Not sure if you can replace them if they get destroyed though.

Late game fleets in GC should be based on what you are trying to achieve. A defensive fleet would be a few medium ships (a couple of Dreadnaught Cruisers), and a load of Light Assault Cruisers (the red corvette). At key planets with level 5 stations, I tend to leave 3/4 Dreadnaughts and 15-20 LACs. I might put smaller fleets at a level 3 station, but tbh it is often not worth it and you just end up sacrificing resources. In those situations it is key to recognise when a battle is unwinnable and retreat. You'll lose the station, but you can immediatley use your offensive fleet to counter-attack. This works even better if you don't invest resources in the defense at all.

Offensive fleets are easy. Use Pride of the Core as your initial ship (it costs no fleet capacity), and then just use mass Venators. A fleet of Pride of the Core, 16 Venators and 2 LACs is the single best fleet you can have in the game. It has more than enough straight firepower to enage anything heavy and all the flexibility of having huge numbers of fighters and bombers.

Tactically the Republic should wreck the CIS fighters as the Republic fighters have shields. I tend to group up my V-Wings/Torrents into 1 or 2 large groups hotkeyed to 5/6. That way I can quickly micro them out of the CIS buzz droid spam before they take any proper damage. With a bit of micro to avoid the buzz droids they will last almost indefinitely, allowing you to quickly eliminate the CIS fighters and then bombers (which are one of the biggest threats to your ships). I honestly wouldn't micro the ARCs over the V-Wings. They are quite tough by themselves and microing the V-Wings more will lead to the ARCs surviving longer anyway.

Hope this helps! If you want any more tips, just ask!

Can someone tell me what ISD means?Maybe ImperielStarDestroyer but there are none in RaW just Victory Class Star Destroyers

Yes, it does mean Imperial Star Destroyer. They do appear in RaW at some specific points.

Oh ok thanks