Wearing the lycra/spandex shorts under longer pants works just fine, it's what I do in the winter when it's cold. The rest of the time I wear a "baggy short", these look like regular shorts but have an inner chamois/bike short built into them. Something like this:
http://www.nashbar.com/bikes/Product...200275_200479\
Cannondale and Zoic are two brands that I have used and are happy with, but try to find them on sale, they are expensive at full retail.