Ministers

[Gandalph]

Most of the ministers are directly linked to the files in the race directory. For example, the ship construction minister follows orders taken from the (race)_AI_Construction_vehicles.txt, the facility construction minister goes from the (race)_AI_Construction_Facilities.txt, and so on. All of the text files are tweakable, as in you can modify them to suit your own style of play.
Some of the ministers are hard coded, like colonization minister will send a colony ship to the planet the AI believes is best colonized. The best thing to do is to play around with them to see which ones you like to use. I will usually turn on the facility construction (after tweaking the file to my liking), colonization, and resupply ministers to limit the micromanagement, especially in the mid to late game.
Hope this helps.

[Baron Munchausen]

Which ministers are you using? For many functions you have to explicitly hand control of the ship/colony over to the AI. Select it and click the 'mask' button to enable the minister to control it. Then you have to have the right minister turne don in the minsiters screen under empire options, of course.

[Gandalph]

For the colonization minister, I turn on the "Automatic Minsister for new vehicles" when building colony ships and turn it back off when building warships, although if you do not have the attack, defense, explore, or patrol ministers on, the AI will not do anything with a warship, even when it has the minister icon.