I can see everything in my file system that I want using the tonido app on my Ipad. It works great; but I can not figure out how to modify the files and get them back in the file system. For instance, I can download a jpg for offline use, and then open it in a sketchbook program and modify it, but I can't find a path for getting the modified file back to the filesystem. What is the normal work flow for this?

We currently don't this support, we only support of uploading photos and videos.
So you could save your image to photo album and then upload via Tonido.

We will consider adding "open in Tonido" for this.

In this specific case, the path will be

you download it to tonido from your computer
you open it using your editing software
You save it back to your photo library
you can then upload it to Tonido using the normal photo upload function

yep.. not the best option but there is one atleast for now until we figure out a way to support it in-app .

What about using WebDAV to upload files to Tonido? Is that limited to videos and photos as well?

You can use WebDAV to upload any type of files.