I am dealing with this on my new boat. One that is hooked up is the water temp sender. It sends the signal to your gauge and tells the ECM how cold the engine it. The other (if it's tan with a black stripe), goes to a water temp switch. This switch sends a signal to the ECM if there is an overheat condition in order to go into "limp mode"
Of course, this is the info that I found out about in my indmar engine with TBI. Your may be different. Also long as your gauge is working fine and you watch it, it MAY not NEED to be hooked up. A dealer can tell you.
The "other location may be under your finger in the first picture; there is a plug screwed into the intake.
1997 MasterCraft 205
2008 Moomba Outback
1999 MasterCraft Sportstar OB
1992 MasterCraft 205
1999 Malibu Response LX
1987 Marlin Magnum Skier