Gee, I don't think you can "glue" those two together but you can definitely use silicone to hold them in place. Just make sure you use silicone for aquariums or a silicone without any anti-mildew additives. Hopefully someone else can chime in with more help.
silicone is nice to use in low-strength apps, since it is not permanent and is easy to apply
but if you need more strength in your bond, here's a little known nugget:
weld-on 40 bonds acrylic to glass quite well
a few years ago, someone on another site ran a test using epoxy, silicone, weld-on 40, & household goop on seperate samples of acrylic bonded perpendicular to a vertical pane of glass (attached like a shelf to the glass)
all samples were allowed to air-cure, were submerged in saltwater for 4 weeks, then were tested for strength
silicone failed at 2.5 bricks
weld-on 40 failed with 12 bricks (pic attached)
I'll not quote the epoxy or goop results, as their potability may be suspect
I've seen a few other instances of the use of weld-on 40 to bond acrylic/glass, including a recommendation from an "acrylic expert", but this experiment really visualizes (and quantifies) it for you
i am also liking Weld-On 4052. this stuff adheres to all of those other plastics that you need to mess with while playing with aquariums. it bonds, CPC, PVC, and acrylic to each other and themselves very well. great for DIY projects.
actually you can glue them together. Home depot sells a glue by 3M thats call "Marine Adhesive". I have used it and It does work pretty well. The only down fall is it takes about 2 full days to cure. I would sugguest using it along with some sillycone. Also Im not too sure if its officially reef safe, but I have used hot glue in my tank with no ill side effects. Just as long as it completly drys before letting it into the water.
i have actually found that if you painted the acrylic with Krylon Fusion spray paint it provides a much stronger bond with the silly cone.
not sure it will hold up like the Weld-On 40, but it is a lot stronger than normal silly cone, expecially after a couple months of curing. at this time is when silly cone will start releasing from the acrylic.
I have had success cutting plexi baffles pretty close tolerence then using a couple dabs of super glue to stabilize then silicone seam on boath sides, works as long as theres water pressure on both sides