Which is better - (3) 12v batteries vs (2) 6v batteries

Hi,

The answer partly depends on the intended use. If you wish to use a large inverter (1500 watts and up) the 12 volt solution, wired in a balanced manner may outperform twin six volt jars.

The 12 volts MUST be wired in a balanced manner for them to work in an optimal manner.

Here is a simple flow chart.

Budget-->Energy Audit-->Battery bank size-->number of watts-->PWM or MPPT.

Here is a link to the rather special spreadsheet that N8GS has created to help size solar battery charging systems!
Solar Spread Sheet N8GS

I do recommend between 60 and 150 watts of panels per 100 amp-hours of storage.

Here are two sites worth reading:

http://rvroadtrip.us/library/12v_system.php

http://rvroadtrip.us/library/solar_install.php