I assume you are drilling into the long rails for bed bolts. When doing that, it is difficult to hit the hole for the cross dowel accurately. The trick is to drill the deep holes first, using something like Dan Gonzales's jig. Then you use another jig to tell you exactly where the hole is, so you can hit it with the cross dowel hole, an easier task because it's not so deep. This second jig looks a lot like the first, except that instead of a hole, it has a solidly anchored dowel that fits into the hole in the bed rail. You can drill a hole in this second jig to act as a guide, making sure the hole is heading straight at the dowel. If you put the dowel into the bed rail hole, the guide will point the cross dowel hole right at the rail hole, even if it is slightly off where it should be.