I have a HDS12-3 with a LSS-2 transducer directly to it. I have read that the LSS-1 transducer is better, I also have a LSS-1 SS module and have read it is better to use it with the HDS12 . Should I leave it as is, swap the LSS-1 in place of the LSS-2, use the LSS-1 transducer and module or use the LSS-1 module with the LSS-2 transducer?

I would stay with the LSS2, but the best option you have with HDS Gen-3 is the SS3D module and transducer. Make sure your Gen-3 has the 18.2 latest software update. You will find your current software level under PAGES - SETTINGS - ABOUT.