I prefer to micromanage the offensive abilities. Things like Telekinetic Push, Cleansing Brilliance and Animosity I like to always make sure are not on Autocast. The AI doesn't always know when the best time to use the abilities, or what the best target is (don't need to use the Push when only a couple ships are around, or Cleansing Brilliance on a damaged Frigate). Using some abilities together, Animosity from the Progenitor Mothership and Cleansing Brilliance from the Radiance Battleship for example is a favorite of mine against a lot of light ships, it requires a human to time it, but it if successful a swarm of Light Frigates can melt away.

Leaving some abilities on Autocast can also end up having the AI eat through your ship's Antimatter very fast, which can be a major problem for the Advent since their abilities make most of their capital ships. This is especially true with the Mothership, the AI is usually smart at using the Shield Restore, but the Progenitor Mothership is very important in keeping an Advent fleet together, so you might not want to risk the AI handling it.

So it really mostly depends on the ship and the ability. Some you really should watch and manage, especially if Anti-Matter is a concern while others you can more or less leave to themselves and they'll handle themselves.

Thanks guys. This helps.

How do you prevent the ships from autocasting? Is there a menu option I have to click on?

When you hover over the ability it will tell you if it's set to Autocast or not.

If you right click while you're hovering over the ability, it will toggle it on/off, depending on what it is set to (different abilities are on Autocast or not by default).

It's also usually a good idea to set your initial scouts to Auto-Explore by doing this, right clicking on the ability, and they go off without management and check out planets until something kills them.

I'm a slow typist, someone already answered.