I had this question too. Apple supports folders in a nice way, but it is not advertised or documented, as far as I can tell.
I figured out how to create folders that I can see on my iPad or my iPhone--through the back door by going into the Library/Mobile Documents folder on my iMac, before I learnedf an easier way to do it on my mobile devices.
Using your mobile device, if you open up Pages, Numbers, or Keynote on your iPhone or iPad, you have the option to see your Documents. If you have documents that fall into a category that you would like to put in a common folder, e.g. "Colorado Trip," all you need to do to start the process is select one of the documents by pressing down on it with your finger, then dragging that document on top of one of the other documents that you want in the same folder. A folder will be created and you will be given a chance to name that folder. After this step, you can drag other documents into the new folder, or out of it if you change your mind.
If you have the most recent Pages, Numbers, and Keynote iOS app updates, you can search your directory on your iPhone of iPad. The search looks inside these new folders, so it's a fairly nice boost to your organization and productivity.
Enjoy!