Heya!
There's not really a lot you need to do to be "Missions Legal". Only three things, really...
1) Be sure to follow the Missions FAQ for character generation and advancement. There's not a lot that's disallowed, but there are a few things.
2) Make sure the characters have copies of and keep the Debriefing Logs for each Mission, included with each Missions PDF, and each character should track their progress and advancement on the Missions Calendars.
3) Players can't play in any non-Missions games with those characters.
As a GM, you should look over the
Missions section of the Shadowrun website. The Downloads link there has all the files you may need.
If you're going to be possibly running at a game store, and they're "open" games (i.e., anyone can sign up and play), look into the
Catalyst Demo Team program. Members of the demo team can earn credit for CGL PDF products and can download the Missions adventures for free from the CDT site.
Good luck, and see you at Gen Con!