Hi there, I have just got the game several days ago and I am enjoying it a lot.
However, I like to micromanage specific things where as I seem to only have the option to do all the work or none.
For example, my biggest issue is I want to customize my own military ships but leave the rest to be automated... can this be done?
It seems that whenever I set the design I either have to turn the automation off or leave it on and have my design reset.
That depends on your game version. With the latest Legends you can pick what to design, if not Legends, you have all or nothing.
If you have Legends (and I believe you need the latest patch as well), you have a couple of tools available.
In the ship design list, you have two choices on the right.
Upgrade decides if an AI designer should mess with the design or not. If you do nothing else, and create a special frigate design, setting upgrade to manual will allow you to have the design around (as an option to build) while the AI maintain its normal design as well. If you build ships from the construction list (part of ship list, or button top right), you have good control as to what to build. Keep in mind that any quick "build frigate" options builds the newest design, which will usually be the AI one.
Retrofit decides if the ship is included if you accept the "retrofit all" option from the AI (or let the AI run retrofits). I also believe these ships ignore fleet retrofit orders (of their fleet), but have not tested...
Setting this to "manual" allows your fancy special frigate to hang around while the normal frigates are updated. This is very useful for powerful alien ships that otherwise would tend to get lost if you could build a ship of their class.
The more clear option is in the empire policy screen.
Some way down are AI options for research and design. You have a list of all design classes. Here you can uncheck for instance frigates, and the AI will never mess with a frigate design again.
It sounds like you want to use the empire policy option to remove your military ship designs from automation.