Do you actually need to "move" them, or do just need to find them and work on the files easily? If you don't actually need to move them, then perhaps a "smart folder" may be the ticket? Sorry, but I don't know your Mac Savy-ness, so perhaps you know what a smart folder and have already determined its not the right solution. But....
If you don't know what a smart folder is, then... it is a folder that has a search function built in, and updates itself in real time. Inside the folder are aliases (shortcuts) to all the items that fit the search criteria. You can open the files from the smart folder, do whatever you need to do, and then "save" the file and it will be saved in-situ. The file never actually moves, the smart folder merely "points" at the existing files.
If that isn't what you need, then perhaps an automator script could help. I'm not a programmer - keep that in mind - but I might be tempted to duplicate your folder structure with a set of empty folders, but nested in a "Working" top folder. Then copy the files from their existing locations into the duplicated folders (by copying you have a back up version). As you work on the files you would then save them back into the duplicate folders. When you were done, then you could then reverse the copying process. Hope this helps. Again, if have already considered and rejected this... well then its beyond any help I can offer.