Multiple cursors with Wacom and Wayland
Solution 1:
Having two cursors when using a tablet in Wayland is by design, but the problem you describe could be due to the fact that you're using X applications on Wayland (using XWayland). Tablet support for X applications under Wayland will be included in the upcoming Xorg 1.20, which will be released in 2018. Until then, you're better of using Xorg. Now, I don't know or use MyPaint myself, so if MyPaint is actually a native Wayland application, my answer does not apply.