Connection to the battery is with 2 wires that have ring connectors on them. You undo a nut on each terminal of the battery, slip the rings on, then replace the nut . That's it.
The controller can be simply placed on a shelf. The display that comes with it: same - or you can temporarily fix it somewhere with tape. There is no need to drill any holes depending on how "zero-impact" you want the installation.
The roof, well, the only way to clean it is to remove the panel. Loosen 4 bolts and slide it off, or if you are very worried about marking the roof, remove 4 bolts and lift it off. It will be cleaner under the panel than the rest of teh roof
The cable is plenty robust enough for continuous movement. Most people will tend to leave the panel in situ for long periods of time.
By default it is always on, but there are two ways of switching it off. You can unplug the solar panel from inside the van. That will stop the solar charging. Or, you can remove the fuse that comes with the kit. That shuts down the whoel kit completely.
Finally - if the two batteries you refer to are already linked to each other, which I suspect you are, then they will both charge together with the solar.