I think generally it is better to leave your PC alone while it is being defragged. I don't think it actually has any bad effect on the defrag process other than slow it down, since it can't move a file while you are using it. This is true the other way around too, you can't use a file while it is being moved.
Also, if you use something like Diskeeper or PerfectDisk, they use up a lot of CPU and RAM so your whole system slows right down.
My advice would be to leave a defrag operation for an overnight job. That way you can use your PC without being slowed down and the defrag can go ahead unimpeded by system use.
SiriusB