The lady at Southwest told me all medication needs to be in it's original container and that anything in a pill box will not be accepted through security. Whether that is correct information or not, I don't know, but we decided that we won't take our chances.
Well, just so you know, it is NOT correct information. If you want to know what TSA will do, ask TSA, *not* the airline. The airline does not have any compellling reason to keep track of TSA's rules, and they quite simply don't have any say in the matter. TSA's word on the matter is here:
http://www.tsa.gov/travelers/airtravel/specialneeds/editorial_1059.shtm
What Anne said is correct, TSA doesn't give a rat's patootie about pills/capsules of any kind, *except* when you hand them packaging that says something like "GELCAPS" -- at which point they will get all bent out of shape over the idea that the pills might be made of gel. You actually attract LESS scrutiny to pills/capsules by putting them in a daily case than when you carry the original OTC packaging. I travel domestically several times a month (on SWA most of the time, fwiw) with my plastic pill case in my purse. I have never been questioned about it for so much as a second.
Make sure that your liquids (including contact lens' solution) or creams in tubes are in original labeled packages, whether Rx or OTC. Size does NOT count for medications, so you can carry the original package even if it is larger than 3.4 oz. For convenience in "declaring" them, it's best to put them in a separate ziploc marked "medications", and put that through the scanner right next to your 3-1-1 baggie.
(BTW, if your pharmacy normally labels the box instead of the tube/bottle, they can make an extra, smaller label that goes on the inside, just ask.)
PS: NEVER, NEVER, NEVER put medications or medical supplies (*especially* diabetic test strips) in checked bags. They are a very popular target for theft, and you'll end up missing doses if you have to get a new supply while travelling. (Also, your insurance company will probably pitch a fit over having to fill them a second time in a refill period.)