need help, engine vs electrical

I have a 2011 Stingray with 4.3 lt Mercruiser ( carb). As I was preparing it for use this summer, I replaced the batteries that I had taken out for winter and kept on a charger/conditioner. It is a two battery one engine system. I replaced the batteries and had marked the cables in order to reconnect the same way it was last year. Last year when I winterized, everything worked fine. Now the gauges and part of the lights seem to be working fine, but much more does not. The radio and all its components are not coming on at all as if they have no power, at least two lights on the wake tower not working, and worse part of all, when I turn the key to start engine I here one loud click ( possibly the relay?) but nothing else. Engine does not turn over or anything just the click. It sounds weird but it seems that anything to the left of the batteries ( direction of one set of wires) works, ex guages, courtesy light, etc. but everything that runs to the right of the batteries does not work, ex radio, some lights, engine, etc. Batteries are good and fully charged. Im new to this and any help would be great. Low budget and trying to avoid costly service charges. Thanks Russell

Absenting a poor connection or corroded contacts on your battery switch, given what you've told us, I have to ask...
Did you "fog" the engine at the end of last season? If not, you may have more serous problems.

When you say 2 battery, one engine, I'm assuming you have a battery switch that is marked something like, "1", "2" "Both"? Also... is everything connected to whichever battery is running the engine or are some loads connected directly to one of the batteries? In some boats ( mine for example) there are the usual heavy cables that go the to engine block (black) and to the battery switch. There are also some loads that connect directly (sorry Ricardo ) to one of the batteries, e.g. the bilge pump and the main feed to the electronics at the helm.

My boat is set up with a "main" battery that is a START duty battery and a second battery that is a "DUAL PURPOSE" battery, i.e., Start/Deep cycle. This second battery runs my main bilge pump and my electronics.

BTW... the "BOTH" position on a battery switch is for emergency use, i.e., when NEITHER of your batteries have enough juice to crank your engine, NEVER to charge both batteries.