Using my shuttlecraft
 

I'm having a problem using my shuttle. I got a free one during a mission with my Kling character, and now I can't seem to figure out how to operate it. I can get to the shuttle's bridge of course, and it appears that the shuttle is selected, yet I can't plot a course or use any controls within the bridge. Is there a command or something else that does this? For example, I need to take my small craft into the Gamma quadrant. I'm in the Bajor System, but I can't figure out how to launch the shuttle.

Once you get to your shuttle bridge, talk to the ship selection officer at the back of the craft. In the lower left corner, choose Small Craft instead of Starship, then exit the shuttle bridge (return to tactical view) and you'll be in your shuttle instead of your starship.

actually, as soon as you talk to the ship selection officer in the transporter room of your normal ships bridge, and select your choice of smallcraft, you are in the shuttle, just return to tactical view and beam up to your ship as normal, you will find your ship replaced by a shuttlecraft.

Any mission that requires you to be in your shuttle will automatically transfer you to it without you having to do anything else. Just fly to the mission system in your regular ship. I'm assuming you're referring to Operation Gamma. Just fly to DS9 in your main ship and click to begin the mission, and it will automatically warp you into DS9 in your shuttle without you having to do anything else.

One important note here. there will be two options when you get to deep space 9. One takes you to the mission, one takes you to the station. Be sure you choose the one that starts the mission.

It's obvious because like Lance mentioned is says "begin operation gamma".

Still, I've seen some people who are so used to seeing bajor and DS9 at the same time, they ignored the second button and kept going to the normal DS9 and couldn't find the mission. So I figure, might be worth mentioning.