Solar Panels with Engine Running

This is primarily geared to those with solar option.   Do you continue to leave solar panels charging the batteries when engine is running with alternator charging?  On my sailboat I turned off the solar and wind when motoring because of the different charging regimens so as not to confuse the external regulator that controlled the alternator.  I have installed a Blue Seas switch which does allow me to disconnect solar if needed.  Any and all advice appreciated.

I'm no expert but from what I have read there is no need.  The batteries will take charge from all sources on the circuit with no need to disconnect anything.  Here is a quote from the AM Solar website:

Do I have to shut off the charge controller when I connect to shore power?
You can have multiple sources charging the same battery bank at the same time.  Whether it is shore power, an alternator, a generator, solar panels, etc., it doesn’t matter.  Connect them all.  Run them all at the same time.  No additional protections or switching of any sort are necessary.  Chargers of all types are protected against reverse current flows and base their output on the voltage of the battery bank they are charging.  When a battery is getting charged by any source, it’s voltage will go up proportional to the amount of current being fed onto that battery.  In some situations where you have a particularly strong charging source, like an alternator or shore power, the high current fed onto batteries will drive the battery voltage up to the point that the solar charge controller thinks the battery is full.  When that happens, the solar charge controller will temporarily stop charging until the voltage returns to a lower level.

And here is there website: http://amsolar.com/diy-rv-solar-instructions/edfaq/  I would trust these guys over almost anyone, they've been doing RV solar for a long time and know their stuff.