From: Ol' Blighty
Hello towerbooks, welcome to the DW forum, glad you're enjoying the game!
I also like to handle almost all aspects of the game and have done from the very start like you! I played my first game taking one thing at a time off of automated onto manual so I only had to learn one thing at a time. Nothing about DW is really that complicated once you get used to it. Ship design is the one thing I have kept automated to this day, unlike the majority of players I'm not really interested too much in this aspect of the game. Plenty of others should be able to help there if you have more specific questions!
As for keeping track of things, remember you can pause the game whenever you want and zoom to the event by clicking or double clicking the message or pop-up. Just remember it is not meant to be played at the pace of a typical RTS, you can play it (and should play it) as slow as you like.
As for repairs. A constructionship can repair bases and other ships. With Legends installed there are two ways of doing this. Firstly, select your Construction Ship and then right click on the damaged ship or base (the cursor should change to a hammer when you hover over it). Secondly select the damaged ship and at the bottom of the screen there *should* be a hammer icon in the little list of buttons. Click it and it will queue a repair order onto one of your constructors! You can also get a ship to repair at a base (or an entire fleet to refuel and repair). To do this select the ship or fleet and right click and choose the appropriate order. Most ships will do this on their own too. You only need to send a Construction Ship to repair another ship if that ship is badly damaged and has no engines left to travel to repair. If it is a cheap ship, and you are not roleplaying that you care about your people, you can just right click and retire the ship immediately to save the hassle of repairing it!
I'm not exactly the best DW player out there, but I enjoy the game very much, so I hope the above helps! My main advice to a new player would be to take things slow and watch your cash, especially if you started on tougher settings (with lower populations and planet quality etc). In other words build something and see if your economy can handle it, not build 50 things and see if your economy can handle it, that will end badly (early game).
"My body may be confined to this chair, but my mind is free to explore the universe" - Stephen Hawking