Nah you don't use the bottle to try and trap the fish like that!!! LOL. You cut off the end that the soda comes out of, then put it back into the bottle backwards... You will have to cut more of the opening off to make it large enough for the fish to swim in.
Once you have the opening inverted in the bottle, put some yummy foods inside of it. The idea is that hopefully the fish will swim in the opening to get the food, then not be able to find their way out. Damsels are smart, so I don't know if it will work for them, but this is the same kind of trap used for crabs and mantis shrimp... Not sure how effective it is for fish.