Mick, first things first, you did not tell us what controller you have, it always assists us to help you if you state what components you nave in your battery system. Secondly, when you say "My rig has a second battery charged by the vehicle," does that mean you have two batteries in the van or is it just using the wrong nomenclature for your vans house battery?

The reason for the common positive build of your regulator is nothing to do with costs (apart perhaps for engineering costs when designing the unit.) In the early days of solar panels, their main use was in the communications industry. The communication industry uses a positive earth system as there are fewer electrolysis problems in their telephone cables with a positive earth system. Most of the cheap (and rubbishy) controllers you purchase from eBay are not well designed models, they are just poor copies of the earlier communications solar controllers. There are very few quality controllers that are positive earth models (Plasmatronics and Steca are two exceptions.) Would I be correct in assuming you have a cheapy from Evilbay?

If you have a positive earth style controller, the first thing you must decide is which one of the three negative terminals is the one that will be earthed to the chassis. The other two must not be connected to the chassis in any way. Anything that is 12 V powered in the van that can not be isolated from the chassis earth must be connected directly to the battery. You can not power them from the load terminal on the controller.

Any 12 V electrical item that can not be connected to the load terminals on the controller will not be metered by the controller. This means that that item will not be accounted for in the state of charge (SOC) metering in the controller. This means that the SOC indication on the controller's display panel will not be accurate and therefore not be relied upon. If you value the SOC function then I suggest you cut your losses and get yourself a quality controller.

If my assessment of your controller is wrong and you have a Plasmatronic or Steca then you can purchase accessories that will allow you to meter the current consumed by the items connected directly to the battery but then they are costly and require extra wiring.

A great post PeterD, thank you for your insight.

I always thought a negative earth produced fewer electrolysis issues which is why the automotive industry has gone that way, although I well remember positive earth cars  from the 1950/60s - one had to be most cautious when buying a car radio to ensure it was the correct polarity.

I can't offer much to the OP except to say that both solar controllers I own are ground isolated and I think that is a sensible way to go with such devices.