I have a zip file that is created using drag and drop on a view in my desktop Flex 4.6 app.
This triggers a service that will automatically upload the zip file.
Embarrassing but I found my answer 42 mins after I posted the question.
A little bit of a rubber duck problem solving going on here.
http://www.codinghorror.com/blog/2012/03/rubber-duck-problem-solving.html
Short answer: Use File class and specifically the method upload which is extended from the FileReference class.
Long answer:
var urlRequest:URLRequest = new URLRequest(PUBLISH_ZIP_FILE_URL);
// set to method=POST
urlRequest.method = URLRequestMethod.POST;
var params:URLVariables = new URLVariables();
params['data[File][title]'] = 'Title1';
params['data[File][description]'] = 'desc';
// this is where we include those non file params and data
urlRequest.data = params;
// now we upload the file
// this is how we set the form field expected for the file upload
file.upload(urlRequest, "data[File][filename]");