I have a fan on the bottom of psu, cpu, and rear case. I want to add a fan in my pci slot at the bottom. I'm trying to help my son's emachine last longer. Can you have too many fans?

As long as you have the airflow going in the right direction, you can't have too many fans. Air typically is sucked in from the front, and blown out the back of the case.

When hooking up these fans is it better to use the 3 pin right to mobo or plug in directly to psu cable?

Some motherboards are better at this than others, but if you plug the fan directly into the motherboard it typically manages the speed of the fan for you (minimizing noise and power usage) so that only when the system is hot, the fan speeds up, and when it is not needed the fan slows down.

I'd connect it directly to the motherboard.

Outside of the PSU fan(s) only a rear exhaust and a front intake fan are needed...