1) buy mono-crystalline panels - best efficiency and not really at a price premium these days.
2) buy a decent charge controller - TRUE MPPT is a good choice to get the most out of your panel.
3) ANY shading of a solar panel will drop output dramatically - so FULL sun is what you want - not under any roof rack rails.
4) You DO want to be able to move the panel a few times per day to track the sun if you want to get the most out of your panel.
Just charge both batteries while you are wheeling and run fridge etc off the combined batteries. The alternator will easily keep up with it all AND charge both batteries.
Switch to one battery when you turn off the vehicle. If you are just sleeping the night etc, then a 1/2 decent aux battery will more than easily keep up with the fridge and other low draw stuff like chargers for ipods/phones etc.
I certainly would not both using a solar panel to charge a vehicle battery while driving along - use the alternator.
I use solar when camped since we may stay in one place several days without starting/moving the vehicle, so a panel that can keep up with average power draw (fridge etc) while camped is essential.
Anything less than 100W panel is really a waste of time in terms of purchasing/setting up/wiring etc etc.
I've made do with an 80W panel and an MPPT charger for two trips to the oz bush now (2 weeks each) and ran the fridge 24/7 off the aux battery charged when driving and topped up while camped for a couple of days.
Typical setup from last year in the west oz bush. As you can see, having the panel on a cable allows moving it to where the sun is.
I've previously used a 40W panel and that was basically not capable of keeping up with the fridge (older Engel) so every 2nd or 3rd day required moving on and topping up the battery. An 80W panel will keep up with a modern Engel etc (the fridges have nearly doubled in current draw efficiency over the past 20 years). In oz a 120W panel only costs $10 or $20 more than an 80W (prices have dropped a lot in the past 2 years) and if doing it again, I'd just buy a 120W panel. More than enough power and will still do a decent job on overcast days. Again, buy MONO-CRYSTALLINE.
cheers,
george.