Good question. It depends who you ask
Basically it depends on what you want two batteries for, you have two options:
1. You just need more current for starting to make really sure it goes on the coldest mornings. In this case you would just connect the two batteries in parallel.
2. You need to be able to run onboard accesories such as lights, night heaters, inverters etc without flattening the battery so it won't start. In this case you keep the main battery for starting and connect all your aaccessories to the second battery. The batteries are connected together via a BIG relay that only closes once the engine has started. The is known as a 'split charge relay'. The relay is driven from the feed to the battery warning light on the dash. This is the system you will probably find in an ex ambulance or police van. In this system the second battery should be designed for deep discharge.
There are many more complex methods used such as baattery isolating diodes or slave charge units. All have advantages and disadvantages.
I have a split charge relay in my van and the second battery is b******d! I am looking to install something more sophisticated that might preserve the battery better but they are all way expensive, like this:
http://www.sterling-power.com/htm/ab1290.htm
Any opinions on this are most welcome.
Steve