When you drag an MI folder to the plugin, it by default renders the frames inside the MiResources folder. iClone sets it one directory higher. This is better and neater.
I wish that I could set a separate render output folder in iClone, like I can from the plugin. This way, I can export the much larger MI files to a folder that won't be backed up, eating up my bandwidth, and render output frames to a folder that IS being backed up. Xfinity only offers me 1.2 terabytes per month. For now, I'm rendering into a drive with no backup. My only fix right now is to export the MI folder and manually drag it to the plugin, where I am allowed to choose an output folder. Operationally, having the option there wouldn't be a problem, nor extra work, for most users.