If the file you are trying to create or edit does not require root privilege, run this:
wine /home/jon/.wine/drive_c/Program\ Files/Notepad++/notepad++.exe
If it does require root permission at all, install the notepad++ with your root account after having been logged in as root (e.g. by executing
sudo -s -H), log out, and run:
sudo wine /home/root/.wine/drive_c/Program\ Files/Notepad++/notepad++.exe
But usually, as has been pointed out, running wine applications as root is not recommended since
wine apps rely on wine and the source code of wine apps may or may not be reviewed, meaning
there is an increased amount of risk involved in doing so.