This is an essential part of setting up and if done properly there will be less stress on the motors and the tracking and guiding (if used) will work more smoothly. With an equatorial mount there are two axies that the telescope and mount have to be balanced in, RA and Dec. The RA is done by adjusting the position of the counterweights on the counterweight shaft. The Dec is done by adjusting the position of the telescope(s) usually by sliding forward or backward on the dovetail joint.
It is useful to make sure that all equipment that is to be used including cables is attached before balancing so the system is properly balanced when you are actually imaging. Absolutely perfect balance is not generally desirable as it may cause the image to oscilate when guiding corrections are made and this is particularly more noticeable with systems that have backlash in the gears, I have read elsewhere that if this is the case then the telescope should be balanced so that the motor is always 'pushing the telescope'. I am fortunate with the Paramount ME in that it has virtually zero backlash.
Some mounts are very tolerant to being out of balance and again the Paramount is a g good example of this in that it can be several pounds out of balance and still track accurately.
Sometimes this can take a while to do properly especially if you have more than one telescope attached but the time is well spent. This is one of the jobs that can and is best done in daylight.