You'll need to remove the old sealant. it will prevent the new sealant from making a strong bond with the glass, and will be likely to leak as well. Stripping the old silicone isn't hard. Just use a razorblade and peel it out. Usually it comes out in long strips.
Once you've got most of it out, run the razor blade along the glass where the old silicone was. You want to make sure that there is little or no residue left on the glass. After that, give it a good wash with alcohol (100% ethanol or methanol) or acetone.
Once its clean and dry, apply the new silicone in a bead around all the corners. Smooth it out with a finger or the back of a spoon. If you want a cleaner look, put some blue painters tape at the limits of where you want the silicone to be, put in the silicone, and while its still wet, pull the tape off. That will leave nice clean lines.