The point to the civilian yards is that you are still going to want a few types of ships under your direct control. There are a lot of ships types that can be done as either civilian or military and the civilian ones don't have a upkeep to deal with. A couple of examples would be troop transports, mobile terraformers and sorium harvesters. I like being able to send a harvester into a somewhat frontline area to establish a fuel depot near the front over time. I also like using civilian troop transports for everything except actual invasions.
The main thing to remember is that the civilian lines build stuff that you have some indirect control over. You can offer a contract for shipping goods, or designate a planet as a destination for colonists. What you can not do is anything more direct. If there are 5 places you want goods shipped to the civilian lines will do them in whatever order works for them and at a time of thier choosing. There are times I need to put things in place quickly, or in areas that have just seen combat. That is where the ships under your direct control come in handy.
Brian
P.S. Civilian shipyards can build ships 10 times as large as a military shipyard can for the same time. Most of the ships that a player wants direct control over that are civilian types are just to big for the military yards to build. An easy example is an early freighter can easily be 40,000 tons while the largest military ship of the time might be 10,000 tons if you are lucky. A decent terraformer could easily be 150,000-200,000 tons. I don't recall any military ships much over 50,000 tons at the highest.
