In addition to checking the polarity, realize that when setup as an ammeter (as opposed to a loadmeter), you'll expect to see both positive and negative amps values, and there are yellow and red ranges on both the positive and negative side.
If that's how you have it configured, and, if you're seeing positive values while discharging (engine off, electrical stuff one) and negative values while charging (engine+alternator running, filling the battery back up after start), then yes you probably just have the ammeter signal wires reversed.
You should also review all of your red/yellow/green ranges to make sure they make sense for your aircraft. SkyView ships with defaults that may not be right for your electrical system.