Just like Dave M. I find that I mostly use the keyboard/mouse and only use a stick for docking etc. or the Powerboat or Jetski. This is easiest (unlike flightsims or r/c model sims). For 'flying I have a cyborg evo converted with homemade rudder pedals and seperate throttle.
It isn't too handy as a Shipsim controller but it doesn't mind when I plug in a gamepad as well - so I find it easiest to set up and use that as my controller. Might work for you too.