I would argue that perhaps both would be best, and have at least two charge controllers, one for each set. One CC would be for the onboard panels, and the other would be for portables. Even if the onboard panel is just 100 or so watts, it is better than nothing, and with the battery switched off, would definitely help keep it topped off, even when stored for a long while.
The portable panels would definitely help out as well. I have seen some interesting solar setups, one of which used three 20 foot long flexible panels staked into the ground, which (when combined with a stout battery bank) seemed to do a good job at providing most electrical services, with the exception of A/C.
