Always read the back of silicone when you buy it. Make sure it has no anti-mold/fungus additives.
GE silicone II is what I used in my first and only glass tank build. But for a smaller application like yours, you can get the special aquarium silicone to be safe.
Silicone does not stick to acrylic due to the oil in it. You can use it for dividers but know that eventually it will let go. I used it to hold plexiglas dividers in my sump and it does work. Just don't know for how long and not recommended for a permanent construction.
I use GE Silicone I Window and Door as it doesn't contain any anti-mildew chemicals. GE II does, but doesn't leach enough to be a hazard on less sensitive fish. Also note that pure silicone takes 2-3 days to cure.