The switch you linked to is the one I use now after having several other setups. An isolator is great and you never have to touch it, but I like the absolute certainty of a switch so I know which battery I am using. I mounted mine right next to my stereo so I can see it when I am right there, and I can easily reach it (or ask the passenger to reach it) when I need to.
Wiring is somewhat dependent on your boat's wiring currently, but generally very simple. How many wires do you have going to each post on your current battery? In a perfect scenario, you have one going to each. In that case you ground each battery to the engine (or connect them to each other and have the existing main ground wire go to either battery), then connect each positive terminal to each side of the switch, and the main existing positive wire to the 'common' post on the switch.
A quick google image search led me to this page:
http://bluewatermarinesvc.com/html/bat_switch.html with a decent diagram of how it should look. Your accessories would also come off the 'common' post of the switch in one manner or another. If you have multiple positive wires, you may not want to put them all on the common terminal on the switch but you might want a distribution block of some kind; the same goes for ground.
Regarding alternator damage, the switch you're looking at has what it calls 'make-before-break' protection, meaning it connects the next battery before disconnecting the one you're coming from, so the alternator is always finding its proper charging field or whatever it is looking for exactly. Just DO NOT switch it to OFF with the engine running. Switching from 1 to Both to 2 and back, it's designed to maintain a connection the whole time, so you should be safe.