I started playing with Protonotes myself, and I agree that it would be useful to be able to automatically insert Protonote code and options when generating a prototype. I decided to take a little initiative myself, and I wrote a script that lets you insert code into the <Head> tag of all files in a directory that end in .html. I've attached the script to this post as a .zip file.
Just drop the HeadInsert.exe file into your prototype directory, run it, then paste your Protonotes code into the text box and press the insert button. For example, I pasted the following:
<script src="http://www.protonotes.com/js/protonotes.js"
type="text/javascript"></script>
<script
type="text/javascript">
var
groupnumber="##############";
</script>
into all of my prototype HTML files.
I recommend making a backup of your prototype files if they are important, as there is no way to reverse the process short of opening each .html file and removing the code you inserted. I am not responsible for anything unexpected that happens to your files. If anything does, let me know (please provide any errors that are given by the program).