What you want to do is referred to as a "leg casing". Instead of zig-zag or straight stitching the elastic down the entire length, you just tack each end and leave the middle free. Then, when you turn the diaper right-side-out, you topstitch down the leg, making sure not to catch the elastic.
Here are a couple of instructions/tutorials (with pictures!), hopefully they'll be easier to understand than my explanation!
http://www.diapersewing.com/hbpocketinstructions.htm
This is directions on how to turn the HoneyBoy pattern into a pocket dipe, but she does the leg elastics the FB way.
http://www.mothering.com/discussions...d.php?t=351652
This is a picture tutorial by the designer of the Fattycakes pattern on doing leg elastics so that the outer material rolls in (for waterproofness

)
http://www.geocities.com/gabrielbaby1/fuzzibunz.html
A guide to making FuzziBunz-style pocket diapers.
HTH!