Allow for serendipity: Other benefits are that sometime as you work, the documents will lead you places you hadn’t planned.
This guide is very helpful for using Zotero in the archives. It does not, however, cover using scanner apps rather than using the camera as your main tool for retrieving images. It also recommends using Dropbox and linking files in Zotero. I think that is one solution, but consider getting a subscription to Zotero anyway. It is not too expensive and will free you up to use Zotero from any computer.
Look over the finding aids in advance. A mistake that some researchers make is to think that because they have a camera, they can just photograph everything and look at it later. You need to know before you go how large the collection is and how manageable it will be to get through.
Predetermine your naming and organizing schemes. Before you even take your pictures, decide how you are going to organize your photos and how you are going to rename the files, if at all. If you plan on keeping them organized in folders that mimic the organization of the collection, use the finding aid to determine which boxes and folders you want to look at and go ahead and set them up so that you can automatically save them to the right folder.
Keep records of what files you plan to look at and what you have seen. You could do this in Zotero, for example, in the record that links the finding aid, or in a separate document.