The things you put in the que give you bonuses to wealth, production, research, etc. So you are being rather productive. Later on the research tree you will encounter terraforming techs which will show you spots to terraform on the planet opening new hexes for you to build on. So you will be able to build on these planets at a later time.

You can also set planetary production to 100% wealth or research. That will prevent the Idle Colony warning from appearing too.

Quoting EleventhStar,

reply 4

This annoys me too especially on shipyards, can't stop making ships unless i remove all sponsors.

And on planets, have to change production to either 0 or move all of it to military, and the having to remember to switch it back when a upgrade to improvements is available.

 

wish there would be a "this empty queue is okay" or "remind me later" button or something. 

You could also set military manufacturing to 0 at the moment to stop all production at the shipyards.

You can remove the que, but the end turn button tells you that your shipyard isn't building anything so stops you from ending the turn. That's why the options are to give the shipyard no sponsors with something to build, or remove all military production to stop the shipyard from building.

The devs already said that they will add a "build nothing" option for the shipyard queue.

Despite that, I don't know what is the better option: build a project like research or wealth, or set the production wheel in the govern screen to zero for the manufactoring but then you have to remember this planet because it will not automatically update your improvements.

It will. After researching improvements they get in front of the chosen project.

Put in one of the four never ending build projects. Then govern that planet, move it's triangle to the edge of the circle on the left or right while keeping the money/happiness where you want it.

If its a manufacturing devoted planet, move it's triangle to the edge of the circle on the left and slam the slider to the left. This will throw all the manufacturing to your shipyard. When you again have something to build on the planet, your going to have to adjust the slider to the right. Lots of micro per planet required to be efficient.

The happiness levels say they change production but I have yet to figure out whats going on.