Wiring them in series lowers the line losses between the panels and the controller (it's amperage - the flow of electrons - that's resisted - and the higher voltage - how hard those electrons are being pushed - helps too). The MPPT controller will take care of outputting the correct voltage to the batteries.
When wiring different panels (or sets of panels) in parallel, the VoC should match as closely as possible. (If producing at all, most panels will produce they're rated voltage, even if they're mostly shaded and producing very low amperage.) If it doesn't, the lower of the two voltages is what will be used, with any difference wasted.
When wiring different panels (or sets of panels) in series, the VoC does't matter much (with an MPPT controller) but the Imp should match as closely as possible. If they don't match the higher-current panel will end up being limited to the same amperage as the lower-current panel with the difference wasted. (If the panels don't have bypass diodes, the same thing will happen if one of the panels is shaded. Some panels, Kyocera for instance, have bypass diodes between groups of cells as well. Some of the super-cheap panels don't have bypass diodes at all.)
There are many references online, some better than others, for the fun of wiring in series vs. parallel, and series-parallel. These are but a few:
Solar FactsMPPT SolarSolar Panels Venue
