Q: Keep file in folder and iCloud?

What is your MacOS X version? If you use Documents in the Cloud (and  did not upgrade to iCloud Drive with iOS 8), there will always be a local copy of the Numbers documents you save to iCloud on your Mac. See:  iCloud: About using iWork for iOS and iCloud

You can create folders in the file chooser dialog, when you save the documents in iCloud.

When MacOS X Yosemite will be released this fall, the iCloud Drive will be directly visible in the Finder, but that is not yet possible.

See:  iCloud Drive FAQ

I see, but the local file isn't precisely where I want it to be, right?  As in, I can't specify a particular file in a folder in Documents to be in sync?

No, you have to store the folders you want to sync in iCloud.

I can't access any of my numbers files and I cannot put any docs in the cloud now. Because I updated my iPhone to os8 I have to wait for a few months to continue using iWork's docs and storing on the cloud?

I can't access any of my numbers files and I cannot put any docs in the cloud now. Because I updated my iPhone to os8 I have to wait for a few months to continue using iWork's docs and storing on the cloud?

iOS 8 would not matter, but if you enabled iCloud Drive on an iOS device and upgraded your iCloud account to iCloud Drive, you can no longer sync with Documents in the Cloud.  It is explained here:  iCloud Drive FAQ

and here:  Be aware, be careful, be prepared for iCloud Drive | TUAW: Apple news, reviews and how-tos since 2004