Just take the silicone and run a bead of it at every seam. You can use your finger to smooth it out and ensure that it has penetrated into the cracks. If you are building a box from scratch, I recommend putting a small bead on the joining edges before you screw them together. This adds strength to the joint.
liquid nail is also a good for running the bead, another idea to insure its sealed air tight is to buy a can or two of spray in truck bedliner and spray that inside the box. Its not much and always makes me feel more comfortable when building the box