Sure, because of the plugin support it shouldn't get too complicated.
You can use strings instead of urls, for files.
So you could do something like:
loadFromS3(function (fileContent) {
j = new Jotted($container, {
files: [ type: 'css', content: fileContent ]
})
})
then create a plugin for it that saves the changes back to s3:
j.done('change', function (err, params) {
saveToS3(params.content)
})
Here's some details about the plugin api:
https://github.com/ghinda/jotted#plugin-api