Apologies I know I'm late to respond to this. RPG Maker requires sprites to be layed out in a specific way to work with the engine. I've never personally used RPG Maker so I'm not familiar with the exact requirements, sadly if you want to use characters from the Character Generator in RPG Maker you'll have to manually change how they're layed out.
In the future I may be able to make a tool/update the Character Generator to make this process automatic.