Unlike other cloud storage services like Dropbox, Apple's iCloud synchronizes documents in use by a specific application so, for instance, in Apple's Pages program you can save a document to iCloud and have it be immediately available for editing in Pages on your iPad or on another Mac. While convenient, this setup does have a restriction in that the documents for one program will only be made available for that program.
While this is not an issue for programs like Apple's Pages and Numbers that have a specialized document format, and may even be useful at times for Word or Excel even though their formats are more widely used; however, for formats that are more ubiquitously implemented in programs such as PDF, TXT, and numerous image formats, this setup can be a bit of a limitation. Therefore, while you might wish to use iCloud's "Documents in the Cloud" feature and have it enabled, in some cases you might not wish to save changes to iCloud and have it manage your files.
Unfortunately when you enable this feature in iCloud, the system will make iCloud the default destination for saved documents in all of your applications, when it may be preferable to have iCloud enabled but use it as a side option for storing documents instead of the default one.
For those who use iCloud there are two approaches for managing this issue. The first is whenever you save or open a document and the system shows you the iCloud document list, simply use one of the Finder's "Go" menu hot keys to take you to a specific folder in your home directory.
In addition to those Apple outlines in the "Go" menu, another convenient one is Shift-Command-D, which will bring you to the Desktop folder in your account.
The second approach is to change a hidden setting in the system to adjust the default behavior for which storage location is preferred. As noted on Cult of Mac, if you run the following command in the Terminal then the system will revert the default storage location to the local filesystem while keeping iCloud enabled for the beneficial services it offers.
defaults write NSGlobalDomain NSDocumentSaveNewDocumentsToCloud -bool false
To undo this change, simply repeat the above command with "true" instead of "false," or run the following command to remove the customized entry entirely:
defaults delete NSGlobalDomain NSDocumentSaveNewDocumentsToCloud
These options should allow you to make use of iCloud while not having it make storing files to your system be a burden.