Yes, you can use acrylic baffles in a glass aquarium. The silicone will not stick to the acrylic however, but it doesn't need to. Put a line of silicone on the glass where you want to place you baffle, then press the acrylic panel (baffle) into the silicone and then put another line of silicone on the other side of the panel, in the corner where the glass meets the silicone. Do this on all sides. You are mainly just wedging the acrylic in using the silicone as a wedge that holds the acrylic panel in. I have built several this way and I have never had a problem. The minimum thickness of the acrylic panel should be at least 1/4 of an inch.