Stoney, I dumped my rule-a-matic switches for their tendency to get crap stuck under them. The V angle between your hoses and the floats don't help either as they form a weir trapping even more debris.
The other rule-a-matic float switches like the Rule 40A would solve the debris jam problem. Rule also makes covers for the ones you're currently using. I believe the cover models are Rule 36 and Rule 38. They're probably $5-6 a piece. That's probably the way to go until the pumps crap out. Which might never happen in a bilge that clean.
Here's another switch that looks excellent by design.
http://www.sealandsanitation.com/sensaswitch.htm
As far as draining both batteries, I'm guessing that they are connected by using 1 battery switch that offers 1 or 2 or 1+2. If that's the case one battery drew power off of the other, draining both. Either separate the batteries by using 2 separate switches, or get the battery isolator I described earlier. It allows you to charge your batteries while under way, but it uses diodes and does not let the batteries to share current unless you move the switch to "Combine" which you only do for emergency starts. About a $100 online. $150 @west marine. Here's what it looks like:
Good luck! -- McGill