Definitely, disconnect the battery before installing new components and make sure that the power is turned off. I'd find a friend who's good with a multimeter, too if you aren't and make sure that wiring harness is not shorted somewhere and is grounded properly. I've seen instances where even with the power switch off, the controller was still outputting voltage. Which can mean a bad controller or system short. You could disconnect the battery, raise the drive wheel off the ground (front, I think on a Cyclomatic) and try reinstalling the controller, then hook everything back up and turn it on. The raised wheel will prevent a runaway bike if there is some other wiring harness issue or if your initial install fried the controller. Let us know how it goes!
Should be @wa5 , please upload a picture of the bike with a couple of shots of where the battery is mounted on the bike; then we can all help you a bit better. Be sure to include where there is some sort of locking mechanism, like a keyed ignition. If it does have some lock, you do have the key?!!