Can I Sync iCloud Drive With Documents?

I'm trying to write a PhD thesis using Pages 5.2 as my word processor. My files seem to save automatically to iCloud rather than Documents unless I remember to save them to the specific folder, which means that I sometimes do not know where to find the most recent version of a file, especially if it's in a sub-folder of a sub-folder. Sometimes iCloud has it, sometimes its in Documents. This is a problem, because I'm constantly updating the things I write and splitting things up into new files.

Is there any way of automatically saving a given file so it's in one easy-to-find location and iCloud and Documents are in sync?

I've tried using Smart Folders, but I'm not quite sure how they work. The various explanations on the internet don't make it particularly clear, and the demonstrations are never relevant for my purposes.

Alternatively, should I simply use iCloud Drive as my primary means of storing my documents?