Generally, ANYTHING will die under concentrated fire from multiple things of just about any type, except for hard counters, like for instance it's pretty hard to kill a capital ship or a heavy frigate (or really anything besides fighters, honestly) with anti fighter ships unless its shields are already down. In general, proton torpedoes are good against everything, except fighters obviously.
The biggest advantage you have over an AI is understanding of organization, AI rely solely on overwhelming you with numbers, and the only time they will launch a well organized attack against you will be by accident. Formation is key, especially in space battles. When you are horrendously outnumbered/outgunned, which you often will be against the AI, good organization can allow you to destroy a force several times the size of your own. Frigates are almost universally less durable than capital ships, and tend to have equivalent or greater range, so they go behind capital ships and usually focus fire on larger stuff while the capital ships pick off damaged ships or chase away smaller ships. Anti fighter ships stay behind the line and break up concentrations of fighters and bombers in order to prevent them from overwhelming larger ships. Keep your capital ships more or less stationary on the defensive, and shift any frigates/anti-fighter units/ bombers (or torpedo equipped fighters) around a lot to help bring down important targets. If you feel the time is right to break formation, try to attack from multiple directions at once to surround and overwhelm the enemy.
Usually, you want to have your most durable units in front, as they will be able to absorb fire for longer than squishier ones, allowing your fleet/ army to maintain maximum effectiveness for the longest. There's only a handful of exceptions to this, the Praetor comes to mind, as that thing's range and firepower are extreme compared to most ships, so, while very durable, you want to keep it off the frontline if you can, since it's most valuable (and infuriating) behind a wall of stuff, firing devastating salvos at enemies.
Mobility is a VERY important factor in both space and on land, and it's the number one reason why building nothing but a huge force of the largest units tends to be a bad idea. You've probably noticed that Petroglyph did a really, really bad job of coding pathfinding in this game. Basically, having a force of nothing but capital ships is equivalent to trying to fit more than one car in a lane, directly next to each other. And don't even get me STARTED on AT-ATs, those things could be on completely flat terrain with nothing around them and STILL have pathfinding issues. On the ground you'll generally want to use air units or light vehicles to scout ahead of your main force and screen any small, agile units that could annoy or flank any large vehicles.