How close should I install J-Channel to a Roof
You're right that nailing so low is a concern. Typically I'd leave at least an inch between the shingles and the channel. If you use color-coordinating step flashing this isn't an aesthetic concern. You can also overlay rubberized window flashing tape on the step flashing to seal nail punctures better. 

You don't say where you are, but I'd worry about melting snow leaking through low punctures in the flashing, or flow and splash from heavy rain.