Now that the sealant has been applied to the underside of the bottom piece, run a bead of sealant around the top of the plastic. Do all three sides, making sure that the bead is continuous and touching both the glass and the plastic at all points. The corners are often a problem - make sure that they are well sealed. Don't worry if it looks messy, as all of the sealant will be covered by dirt eventually. You can use your finger (wrap a piece of paper towel around it first to prevent direct contact with the silicon) to push the silicon into place if necessary.
Once you have gone around all three sides of the bottom, place a line of silicon along the open front edge, slightly back from the edge. Also run a vertical bead up the sides of the tank, to the same height as the vertical piece of plastic. It often helps to test-fit this and draw a line in the proper location, as you did for the bottom piece.