Make sure you clean the edges where any old silicone was, when you think you have cleaned enough clean some more.
Wipe every surface down with alcohol a few time to remove any oils, finger prints and wear latex gloves
Work fast but careful when you run your bead ensuring no air pockets or starts and stops
Get panel in to place and clamped then immediately run your inner beads and smooth out.
Great tip is to use painters tape on the inside of the glass panel where your inner seals will be, allow enough space for the smoothing process and wide enough seal. Then immediately peel the painter tape off giving you smooth straight lines.