Since you're running directly from a battery I would say it's safe to just add as much decoupling (in other words caps across your input power) as possible, since the only real downside (that I think is relevant to your setup) to adding a lot of capacitance is increased in-rush current (since the capacitor naturally acts as a short-circuit during charge-up).
In certain circumstances however the high current draw associated with excessive decoupling during initial start-up should be avoided. An example is when you use a switching converter to step a voltage up/down. If the converter has built in over current protection (and no slow start feature), the short-circuit caused by the uncharged caps will cause the converter to stagger (starting up, over current and starting up again), and never fully reach its target voltage. However, since you're running directly from a battery this shouldn't be a problem, since a battery can be driven way above it's rated current capacity (for short periods).
Another thing to also remember is that since there exists a large energy store across your power rails (the capacitors), the system might take a while to discharge (after being powered off). In other words, your Pi will probably run for another 30 seconds (depending on how much capacitance you add) or so after you disconnect your main battery.
Finally, always try to add capacitors that's rated at at least twice your operating voltage (for instance, if you have 6V batteries try to get 16V caps). Motors that reverses their direction very quickly may induce sufficiently large voltage spikes back into your system, and cause your caps to explode (hopefully your motor driver has sufficient clamping diodes).
I would say a single 1000 uF electrolytic cap would be more than enough decoupling. If your Pi continues to brown-out, I guess the more appropriate cause would be your batteries not being able to supply the required current. Remember, the reason you Pi is restarting (or browning out) is due to the supply voltage dipping because the batteries are unable to supply the current the motors require. Adding capacitors will help with surges in currents (such as motors accelerating), but obviously won't solve long term high current draw.