Like others have said, sounds like your problem is in electrical pickup, not the turnout itself.
However, if you're still interested in powering your frogs, just check out:
http://www.wiringfordcc.com/switches.htm
Dan Stokes
My other car is a tunnel motor
baron9,
In search box input 'insulated' and 'frog' and result will give you multiple responses re this subject. Some even have links for more extensive explanations.
Your AC6000 should be able to bridge your #6 Atlas turnouts. I have several BLI locos and some very old Atlas switches and have experienced no stalling problems at any speed. It sounds like your units are not getting all the electrical wheel pickup they should be. Only problem I've had with BLI units re pickup is first run Hudson-that is another story altogether.
Jon