If you want to continue to use iOS devices to edit or create documents and have them accessible to other devices and now the Mac, using iCloud is your only practical choice. There is nothing special you need to do on iDevices to save them to iCloud. That's where they go by default. On the Mac, however, you have a choice of saving them locally or on iCloud, so be aware of this.
Loosing a document is not normal, neither is them not being synced. We would need a lot more info to de-bug this. It is possible to disable iCloud Drive, as you know, but I do not advise doing that. There are many other, third-party apps that may rely on it to store their data, in addition to those made by Apple. Just make sure you're settings are the same on all devices and that you use only one Apple ID across all your IS X and iOS hardware.
One practice that might ease your mind, is to open the iCloud-saved, iOS-created documents on your new Mac. This will create a local copy of the document.