It really depends on your kit. Which one do you have?
Generally speaking, splashing with water won't cause too much of a problem, I've ridden in the rain a ton. A couple things you can do are filling the back side of your connectors with silicone or hot glue and ensuring you have a drip loop in the wires to your motor. Also, make sure the wires to your controller exit down and not up. If they exit up, water will run down the wires and into your controller.
A bigger problem than water getting into stuff is water STAYING in stuff. Some guys wrap components or connectors in cling wrap. Not only is it impossible to 100% waterproof this way, but it also means any water that works it's way in will not be able to get back out and will corrode things even worse.