With the Presenter plugin, you can do the following to get a single output file:
When you publish your Presenter project, you can choose to publish to a SWF (Flash) format or HTML5 format and this will generate multiple files in a single folder.
There is also an option to generate a single zip file, so that you can upload one file to your LMS.
However, if you want a single video file (MP4) as an output you can do that with Presenter Video Express (PVX) . If you have purchased Adobe Presenter, this tool comes along with it (and it is also available as a standalone separate product). This tool captures whatever is there on the screen as well as the webcam connected to your computer simultaneously, and post-capture it will allow you to mix these two streams as you wish to create a single video file. Here are some short video tutorials that explain what you can do with PVX - Introducing Adobe Presenter Video Express 11
It is important to note here that, PVX 11 also allows you to add in-video quizzes and when you publish such projects; it also generates an HTML player along with the MP4. The quiz will be available only when you play the video with the HTML player we generate; which means that you will have to deploy the MP4 along with the HTML player to your LMS or web server.
Finally, if you installed any creative cloud product or Presenter 11 you should also see Adobe Media Encoder installed on your machine.This tool can be used to convert video files in one format to another format.
Hope this clarifies and answers the questions you may have.
You can output a ZIP of the output files and then upload that to your server. Some servers will unpack it and deliver it for you, or you may need to un-zip it once it is on the server and then point to the index.htm file. Presenter has no option for a video file to be output.
You can also output as a singl page PDF with the Presentation embedded in it, which does retain all of the presentation functionality, except attachments and some reporting functionality. It may be worth trying and seeing if it meets your needs.