The data folder is located at C:\Users\$USERNAME$\AppData\Local\MatterControl (AppData may be hidden). Its location cannot be changed.
In ...\Local\MatterControl\Library\CloudData, you'll find the local versions of the files uploaded to the Cloud Library. The filenames are nonsensical characters, so sort by 'Date Accessed' to find recently added files, since 'Date Created' is only whenever the original file was created.
To edit the remote files (or, tidy up), you'll need to use the MatterControl interface, or head over to the Sync Dashboard: http://sync.mattercontrol.com/my/library/
At this time, moving files to folders is not supported (*shields head from random objects being thrown at it* -- yes, I know), but it is on the list of future improvements to this system. In the meantime you'll just have to download files, then delete them, and finally re-upload them to the folder you want them in.