Hello Arduino World,
We are working on a project that requires us to connect a vacuum pump of the 6V DC variety to an Arduino Mega board. If anyone has any insight on which pins to connect the wires to, we would appreciate your help.
Thanks! 
To provide specific advice we need to know the current requirements of the pump. The running and stall current, as a minimum. You cannot connect the pump directly to a digital output as it will certainly require more than the 20-30 mA that an output can safely provide. And the output will supply Vcc (5 volts?) at most. Assuming that the motor will run in only one direction the options are: motor driver module, mechanical relay with transistor driver and flyback diode (or a relay module), DC output solid state relay or logic level MOSFET. The easiest and cheapest, I believe, would be the MOSFET To size the MOSFET the stall current (max current ever required) must be known. Stall current can be estimated by measuring the winding resistance and calculating current by:
current = supply voltage / measured winding resistance.
You can't directly power a motor from the Arduino. You'll need a transistor, MOSFET, or relay, etc. And, the pump needs it's own 6V power supply.
[u]This example[/u] shows a solenoid, but a pump motor would be the same.
You can choose any I/O pin and configure it as an output (for connection to the transistor/MOSFET).