I have never applied GS to silicone that hasn't dried. I would recommend just letting the silicone cure before adding GS on top. However since I haven't applied before the silicone cures I would not know if it there is a negative to that method. Try testing it on some scrap cardboard and see if there are any benefits or negative results. Post back if you do!!! This is interesting and has a possibility of saving time. Until then allow your silicone to cute before working further--
What I do is silicone egg crate to the glass with just a few dabs here and there and that way I don't have to wait a whole day to start the great stuff. I can do it the same day. It also will save me if I ever need to tare down the tank to not have to pull off all the silicone from the glass.
If the silicone is not cured before applying GS, then as the GS expands, it moves the silicone and shows through the glass. (and that is why I apply the silicone, so I wait the 24 hours for the cure.)
Another method I have used for small sections of great stuff is apply it straight to the glass, let it dry, then peel it off the glass and silicone it back on. This way you dont need to spread so much silicone and the glass stays clear where there is no foam.