Why are the files in acrobat.com not organised in the same way as I organised them in my iPad?

I recently activated my cloud account in Acrobat.com. I was informed that this means the files I have in my iPad Acrobat Reader will be available online in Acrobat.com. However, when I accessed the website on my office PC, some of the files showed up but not others. Worse, they were not organised into folders the way I had organised them in my iPad. Can someone tell me why this is so? Is it because some of my files have yet to be automatically uploaded? If so, why aren't they organised into folders? Oddly, the files I see in Acrobat.com were originally in one of the folders in my iPad. I have some loose files on the root folder but they are not shown. Please help.