you just fly to the planet where you have to do them and if you click on the planet or location then the mission gets fulfilled if you have the necessary stuff on board. There should also be a exclamation mark next to active mission sites.
Okay so I have a mission where I need to get 34 copper ores to the Iltari Space Station, I have the copper needed, but I keep flying there and nothing happens
That is quite unusual. I assume you have the necessary amount of copper ore in your cargo. I will investigate if there is an issue which prioritizes docking over completion of missions. It's the only thing I can imagine causing it.