Using mana box is great. If you happen to have a lot of a particular set laying around you can have it just searching through a set and it goes really fast. It's not great at getting foil vs non foil, but you can update that as you go. Then you add that file to moxfield.

Also it doesn't like duplicates right after another, so a messy collection is actually fine. There is a specific file type for uploading to moxfield. It's a great little app. I use it regularly.