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Within the last year I've flown out of both Hobby and IAH with a pistol, and it has been nothing more than an annoyance due to the line. I see you're in Houston, so I'm just assuming you'll be flying out of here.

Easiest way is with a locked hard-sided case that fits in your suitcase. Personally, I use a two-gun box that I picked up at Academy some years ago that looks like a Pelican case. It's big enough to take two pistols and the magazines for them.

As for the ammo, the easiest sure-thing is to unload the mags and put the rounds into an MTM-style (reloader's) case and carry them like that. I have on numerous occasions slipped the loaded mags into a mag pouch and flown that way...but I always carry the extra MTM box on the off-chance that someone decides to blow a gasket at the ticket counter...I just get tired of loading and unloading magazines :)

Houston airports are very familiar with the process, and I'd guess that every ticket agent deals with it daily. Other places, not so much. I've learned to carry a printed copy of the FAA regs and the airline's rules for my return trip. On the rare occasion that there's a hassle, you'll probably know more about the regs than the folks charged with enforcing them.

I've received several "attaboys" from the gate agents for having the case-within-a-case method, apparently it makes it easier on them, and by doing so my gun case gets the "special" tag, and my suitcase doesn't...but it does get flagged as screened...and so it's always one of the first on the baggage claim, and it never picks up extra search tags.

Expect no hassles, a few delays, and be prepared to educate someone if necessary, and you'll be just fine.