I traveled for the first time out of the country, requiring a passport, last year and had similar concerns.  I get a number of my medicines mail order (90 day supply), that comes in rather large bottles.  Several websites will tell you to keep your meds in original containers and/or carry a copy of your prescription with you.  Several "seasoned" travelers told me that as long as you have just what you need for your trip, you shouldn't have any problems.  I carry my meds in a seven day pill organizer in my carry-on, in case my luggage and I get seperated.  I didn't have any issues traveling that way to Europe for a week.  Third world travel or longer periods of time may require the "official" method of prescription carry.  
_________________________
The Seeker