Hm, I have to ask, what benefit are you hoping to gain from having the worm bins in there like that? Do you have too much material for vermicompost to bury directly in the gravel bed? Most people have worms in the grow bed eating the fish poo and plant debris that accumulates including dead roots, etc. The worms get quite active and reproduce a lot.

Depending on how the chlorine is in your water, it is common practice to let it sit for a few days. It depends on the water temperature, if it's in the sun, and if you are agitating the water surface. If you have chloramine, take a Vitamin C pill, crush it up, and throw it in the water.

The bacteria you buy at the pet store is just bacteria, basically. You can double check the MSDS of the specific brand you get or call the mfr.