When I got my boat, it had a single battery. I bought a second battery as a backup; it wasn't connected to anything and had to be manually charged every so often to top it off. That got old fast, so I decided to add the second battery properly and separate starting and other electrical needs. Lights, radio, GPS/depth finder are now on the second battery, while the first is dedicated to starting (and a backup bilge pump).
I thought about connecting the batteries using a simple Off-1-2-Both Perko switch (as described in the article link you provided), but it sounded like it would be pretty easy to accidentally discharge from both batteries by forgetting to change the switch.
Although it's a bit more expensive, I decided to go with a Blue Sea Add-a-Battery kit (
http://www.iboats.com/Add-A-Battery...2066984--session_id.082095076--view_id.730150). It provides great peace of mind; I can now run electronic equipment off the house battery and save the starting battery. The house battery also serves as a backup in case the starting battery fails.
The nice thing about the Blue Sea kit is that you basically set it and forget it; the batteries are separated for purposes of discharging (so you won't drain your starting battery because the radio was left on, for example), unless you override it and combine them. When the engine is running and the alternator is generating electricity, power will be sent to whichever battery needs it, without have to set any switches manually. It couldn't be easier.
If you do add a second battery, be sure to get proper cabling. There are a number of companies that sell custom made cables using tinned copper wire (to resist corrosion) with whatever sorts of terminal connectors you want. They aren't any more expensive than buying wire yourself and trying to crimp on connectors. You can specify exactly what you need and have them delivered within a few days. It makes the job much easier.
Good luck!