There's no easy way as far as I know.
Since you're using opie-handwriting however, which is open sourced, you or another developer could add a feature or simply tweak the size to make it bigger and recompile. It will reduce the window area available for applications though.
What we could do with is a transparent full screen input method that works similar to Jot on Palm, which does a good job of distinguishing when you are trying to write and when you are interacting with an application.