For me, like a lot of people, the iPad's change in the paradigm (beyond just using touch instead of a mouse) presented some challenges to my normal way of thinking. Unlike (apparently) a lot of people, however, I kind of enjoy these sorts of challenges (sometimes it takes a while to enjoy them, but I do) -- too much time in museums, theatres and other dark rooms with odd people, I guess!
-- so I found that what really helped me was to stop thinking in terms of files and folders. After all, its an invented metaphor based on office work, and I wasn't using my iPad for office work much then.
At that point, the realization that all "files" created on an iPad stay with the app instead of being filed separately (in most cases are literally stored inside the app package!) was a revelation. On reflection, this seems like the most logical idea in the world! My tax returns are in my tax app! My writing is in my writing app! My drawings are in the drawing app! Photos are in a Camera Roll, that every photo app I might use or try out has access to. This makes total sense! It's folders that are stupid!
Of course, in truth both systems make sense, just different kinds of sense. It's like saying the Chinese are idiots for having invented chopsticks instead of forks. Once that revelation came to me, I started using my iPad differently -- unconsciously allocating certain tasks to the desktop computer with its mouse and keyboard, and others to the iPad. There is some crossover, of course -- with a keyboard case I can write all day long in a coffeeshop if I need to, but I guess I just decided (again, not really consciously) to use the Mac for what the Mac is really good for (moving quickly among tons of apps or windows, like when I'm writing something that needs a lot of research) and the iPad for what its really good for (mostly passive activities but also things like drawing, photo improvements/cropping, dealing with email and the occasional bit of music creation). I stopped wishing the iPad was a Mac in some ways, and the Mac was an iPad in some ways.
I'm not saying this is the right path for everybody, but it was successful at stopping me from having any stress over things that are difficult to do on an iPad but not difficult on a Mac, and vice-versa. Now they are more like two helpers, the cook and the landscaper, to me. You wouldn't ask them to swap roles and expect the same level of success.