Moving Folders using iCloud
This isn't the "supported" procedure, but there's a good chance it will work to move a large number of documents to iCloud.

You still have to move documents kind by kind, but not within particular programs.

In the Finder, select the documents (not a folder; the Pages (for instance) that are in the folder) that you want moved to iCloud.

Select Copy from the Edit menu.

Press ⌘⇧G to Go to Folder.

Type ~/Library/Mobile Documents/

If the folder com~apple~Pages exists, double-click it; if not, create it then double-click it.

Select Paste from the Edit menu.

Repeat for the different kinds of files you want to open in their respective apps via iCloud.