I was wondering what was the best way to cut some storage areas in the deck of my jon boat so the covers hinge open. Not sure how to go about this.

Hard to say without seeing your boat. What material is the deck made out of? How solid is it? I customized my jon boat and built the decking out of PT plywood. To install storage, I cut out the door, trimmed all around by about 1/2-inch to accept carpeting and then installed with hinges (can use piano type like in a bass boat or door type). Will have to have some support underneath though for holding the lid in place. I used L-angle aluminum bracing on mine, but you could use other options depending on your exact setup.

Another possibility is to just build an add-on storage area in one corner of the floor of the boat. This would be pretty simple and easy, as long as you have a little room to spare. You can get an idea of these different suggestions that I used by looking at the pics in this thread I posted.

http://www.bassresource.com/bass_fishing_forums/YaBB.pl?num=1209601311/0#0

-T9