The turn button is multifunctional. It is basically a auto check/things to do list for you. It the turn button is telling you that something is idol or needs attention. When playing with lots of planets or even ship yards it comes in handy. You will notice your turn button -lower right corner- saying "shipyard Idol", "idol colony", "research" or idol ship. When all those tasks are completed you can complete the turn. I usually cycle threw the check list first until "turn" comes up then micromanage were I feel it's needed then it hit turn.
As for the ship yard you can double click on the left side were the ship designs are to start producing the ship of your desire. On the bottom right of the screen in a box you will see the ship name that you chose and how many turns it will take to produce.