For dead bait I use either tripple gang hook or 2 single hooks. The gang hook is self explaining. The 2 single hooks I rig with one direct on the end of the line and the second about the length of the bait up the line. You can do that by using a loop in the line or a small dropper set up. Or simply tie the first hook with a long tag end use the tag for the other hook.

Live bait should only have one hook. Be careful not to go through the spine. I usually pin the bait just in front of the dorsal fin. But you can also pin it in either the top or bottom jaw with good results. Or the tail can be used but be careful not to pierce the spine. A lot of predatory fish will strike the tail first to disable the prey before coming back to finish it off. Ambush predators will engulf the whole bait in one go.

It could be a case of a predator disabling the bait. Try to just leave it there after the first strike. If it takes out the bottom (belly) of the bait it may very well return for the rest with the hook in it.