Short answer: Yes. To be honest, there's less a player can do economy wise and more that can (and needs) to be done military wise. If you want to set up your fleets so that you're not tearing your head out, you need to do a few things.
A. Leave it ALL to the AI, which'll be sub-par at best but you won't feel like you're fighting your own units (most of the time).
B. Here's my method for setting up fleets.
1. Turn off automatic fleet formation. If you leave this on, your automated fleets will keep shifting their postures and doing stupid stuff.
2. Only produce ships from the build order screen if you want to build non-fleet freighter escorts.
3. Build whole ship groups together, preferably at the same shipyard, from the military ship/construction yard screen. Group them into fleets from the military ship screen while they're being constructed.
4. (Optional) Name your fleets so that you'll remember where you put 'em. I use a task force system like this:
1st Fleet, TF-1 CWD [Capital World Defense, 5 Caps, 10 cruisers, 3 carriers]
1st Fleet, TF-2 RRT [Rapid Response, 5 cruisers, 10 destroys, 2 carriers]
1st Fleet, TF-3 RRT
1st Fleet, TF-4 OFF [Offensive, 5 caps, 15 cruisers, 5 carriers]
1st Fleet, TF-5 INV [Invasion, 10 cruisers, 5 transports, 2 carriers]
5. Send out your fleets, set their postures. Make sure automation is on. Be sure that there places where they can refuel nearby. Resupply ships are great for providing fleet refuel for newly established frontiers:
The 1st Fleet is meant to protect my capital system, and the two systems in the neighboring sectors. TF-1 is stationed right on my homeworld, with Defensive Posture, System. TF-2 and TF-3 are each station at the other systems with Defensive Posture, Sector.
I have a similarly organized 2nd Fleet stationed around some systems I conquered early in the game, a cluster of habitable worlds around six sectors from core cluster. The 2nd Fleet is larger and has 3 more RRT task forces.
I have a 3rd Fleet with PAT (patrol) task forces made up of destroyers, cruisers, frigates, and carriers to patrol my frontier 10 sectors away. They're support by three resupply ships deployed to nearby gas giants since none of the colonies have the resources to build the star ports necessary to support the patrols. The civilian freighters don't bring in enough fuel for the ships to rely on the colonies.
Even with these precautions, some baby-sitting will be necessary to keep ships from crowding and clogging at mining stations or empty colonies.
Hope that helps! And trust me, organizing your fleets in Shadows is really fun, especially when you see your named fleets zooming off to crush some bugs in the galaxy view.
< Message edited by Dotdotdot -- 7/2/2013 7:40:05 AM >