I can't speek for the ANG/RES, but as for the airlines here's what I found. Most airlines work one of two ways, they either want you to bring the letters to the interview or they want online recommendations from inside their company.

So go ahead and apply at all the airlines you plan to work for, most do it online nowadays. Some will require Rec's from inside, get those, no need to tell the boss yet. Then when you get the call for the interview, tell the boss you have an interview with XYZ and request a letter.

At this point you should know who to address the letter to i.e People Dept, Chief Pilot, etc. Most Bosses I had, did not want me to write the letter, but they did want a good list of accomplishments, format, and who to address it to.

So I found it best to give them a package which included a sample letter (electronc), mlitary style bullets of my career, and a resume. I would make the sample close to what you want for the real thing.

As far as how the boss is going to take it, I wouldn't worry about that. If you're a good guy and served well, the boss will understand. I've seen all kinds of things happen to guys researching their options, some get hammered, but most don't. I've seen guys go all the way through the process, land a good airline job, and then decide to stay in. Most good commanders out there have been through the decision process you are going through and understand ultimatley you are going to do what is best for you and your family. If you get the one who doesn't understand, well too bad, nothing you can do about that.

As For the ANG/Res vs Airline, I'm sure you probably already know this, but the two resumes are very different for the two different kinds of jobs.