From the way you've written it I assume that you've used a battle event. If so, then there are two ways to do this.
1 - Make your skill call a common event, and make this common event activate a switch. Then, in your battle event, set the condition to run to "Switch [whatever your switch was] is ON" and make the character transform. Alternatively,
2 - Make the common event your skill calls do the transformation itself, applying conditional branches so that it can only be used in the appropriate battles. This method is better because you don't have to write it into every battle you want it in.
If you're not using a battle event, and just a common event, then follow method 2. Hope I've helped and not necroposted!
AP (HP).