I LOVE making ruffle jeans and have had to make myself stop b/c all my dds jeans would be ruffled! Here are a couple of options:
1. roll hem the jeans underneath b/4 putting ruffle on
2. i always sew a 7/8 inch ribbon on top of the ruffle that's showing and I sew this right next to (1/4 inch) from the part I cute off and do a tight stitch around them-this keeps fraying to a min. and you don't have to hem them.
3. Or, something I intend to try is the thread by pricess stinky pants on here that had a new way to hem jeans without taking up the originial hem.
HTH! Let's see pics of yours!