When you design a ship, you can see it's PPV value. It's possible that your patrol ships have such a tiny PPV value that you need to build more of them.
Check on Colony screen how much PPV your colony demands and then compare to your patrol ship fleet.
If a Civilian Mining Colony is operating on Mercury, you can buy their output - this is usually the best way to proceed. You cannot remove them per se, but you can also put down your own mines on the same body.
Creating an empty colony on a body prevents CMC's from starting there so that's how you can reserve certain bodies for yourself.
Cargo Shuttle Bay is part of Logistics research if I remember correctly.
Ground troops and interstellar movement are quite complex topics - there are plenty of tutorial videos available here on the forums, you might want to check them out.