I have not used a mc pipette for qPCR. But if you want to do so, your pipette needs to be of very good quality, calibrated and capable of dispensing accurate volumes through each channel. A very minute change in volume may result in significant deviations.
like the other answer, i never used a multichanel pipètte for q-pcr (needer for normal pcr), so i think that you should try to avoid use it, and if you can´t do anythging else, you will have to take care (extremely care)
I hope that you find a solution, and you can understand my not native english
It is tedious to use a single channel pipette, but at the end of the day you will appreciate it. With a multichannel, unless it is perfectly calibrated, the Ct between the replicates may vary. Small volume changes involve variations in the amount of cDNA dispensed, which will cause earlier or later detections of your amplified product relative to the true value.
Also, remember that you are performing a quantitative technique. Being as precise as you can is a requirement. Your results will thank you!