Dave, I feel your pain. In our maiden voyage in our R29 and my first time trying to pull into our slip, the stern thruster was overpowered by about a 15 mph wind, and I just about hit our new neighbor's boat. Luckily our friends and previous owners were with us and took over the helm to get the job done. I had another very difficult time trying to get off the dock at Sydney Spit where we were tied on the starboard side and had about a 15-20kt wind pushing us onto the dock from the port quarter, boat in back, boat in front. For that one, I kept on the thrusters for probably too long, and more or less pivoted off the starboard swim step and dinghy. In hind sight, we should have used a spring line and the thrust of the prop. and rudder to get the stern off, then back out (though I still haven't tried this). Since those experiences, I've really been practicing using the thrusters as minimal as possible, and that has helped a lot. I hope to have some discussions at the upcoming Roche Harbor Rendezvous about how to better handle the boat when docking and coming off the dock in windy conditions,with our limited power stern thruster. Can be very stressful in those situations! This is the one thing that has kept me from adding drop fins, as it appears the stern thruster would just blast into the fin, really rendering the thruster almost useless.
I like the suggestion about having the bow & stern thrusters run off different battery banks.