First off, tell us which type of waders they are. If they are breathables youll have a much easier time finding the hole.
Take your breathable waders to your bathtub, or a river/lake and hold them under water without letting any water get in through the opening of the waders. Hold the waders there for a couple minutes, keep your eyes open for bubbles, now pull your breathables out and there should be a darker shade around the area with the hole.
If you decide to use aqua seal be very careful applying it, and dont not use too much. Using too much could make the leak even worse, as it will hard that area on the wader and if the seal is ever bent will crack your waders and the problem leak will be 10 times worse, this is worse for neoprenes.
*One problem I should warn people of is to watch for too much rubbing on the neoprene footings. If you notice alot of gravel in your boots after fishing, or your boots dont fit properly, or your boots have a rough edge inside then make sure you get something to protect your neoprene footing from abrasion. I use plastic bags, but I have heard of others using socks. I wish I had known this when I had bought my first couple pairs of waders.....