Normally I would only use a megger to test in a troubleshooting scenario if a mulitmeter test looked good, and all the obvious stuff is ruled out first (mechanical binding, single-phase conditions, VFD problem). Then I will remove the motor leads from the power source. This is very important when dealing with a VFD (or any solid state) driven motor. Our megger has a 500v and a 1000v setting. I connect one lead of the megger to all the motor windings and the other to ground and test the wiring and motor all together for ground faults. Then, if indicated, you can isolate at the motor to determine if there is ground potential caused by a contactor, terminations or wiring, or the motor itself. Never connect the megger to any electronics. Contactor contacts are okay to megohm test, but not drives.
I have seen a regular Fluke 99 show 1 megohm, and a megger showed 2 kohm on the same motor. The high potential of the 1000v megger can reveal defects not possible with a standard multimieter.
We are supposed to be using the megger as part of our planned maintenance program to chart the readings of our larger motors. This info is useful to predict the end of life of windings. When done regularly, just before serious problems arise, there will often be a sharp drop in phase to ground resistance.
Like Ron said, if it checks bad with a multimeter, then you don't need the megger. I check for ground faults with a meter in the same way. One lead on a good ground, and all motor winding leads tied together on the other lead. Usually 1 megohm or higher means it's okay. Also check resistance of each winding. They should be balanced, but the resistance can vary greatly from one motor to the next, or even between different sets of windings of multi-speed motors. If in doubt, compare with specs, or another known good motor.
In my experience, more than 90% of the time, if it checks good with a multimeter for both of those tests, then it should run when powered correctly.
Being VFD driven the best way to check the voltage and current output of the drive is with the drives keypad/display or analog output if available. It's not practical to measure voltage of a VFD output with a multimeter. Even the best Fluke meter we have is inaccurate when hit with the carrier frequencies present on VFD power signals.
Paul C.