I don't think you'll be able to do edits much more sophisticated than the cut-n-paste. It's not like you'll be able to insert a sentence somewhere and have either the scanned image or the Wacom-captured stuff word-wrap accordingly.

If you wanted to keep the handwritten look and still make reasonable edits, I'd either stick with the Wacom and use whatever photo editing or illustration software you want to do direct changes, or else go back to scanning with a couple of potential changes:

1. Consider changing paper to an engineer's computation pad. It's gridded on the back side so that if you photocopy it, the grid lines won't show up on the copy. In your case, you could use it to keep your text lines parallel, sketch out graphs, etc.

2. Even though the computation pad would probably be green or beige, a little editing work to convert it to greyscale and then to threshold or posterize it to wash out the paper color to pure white would make it ridiculously easy to move around lines of your solutions in case you needed to add more steps in the middle.