Just mix the JB Weld together per instructions first, and then it's fine to apply underwater. And 'Yes', it's safe for fish and corals.
A couple of friendly tips:
1) I agree with billdogg. If you can get the rocks nice and secure simply by stacking, that's the way to go. Sometimes the cured epoxy putties can easily be broken loose, but sometimes they can also be rather difficult to break apart. If you ever need to remove/move any rock around, you will have to deal with the cured epoxy unions.
2) However, if you go ahead and use the JB Weld, I would use small amounts - just enough to secure "pressure points", and place the putty in such a way to be as out of sight as possible. Coralline algae will eventually grow over the epoxy putty, but until then, the putty can look a little unsightly.
GL! :bigeyes: