Can you publish once for LMS and HTML 5?

Hi:

I would like to publish for LMS for folks to use their laptops etc...and also have the course published for use for folks using their Ipad...however, I am wondering if I have to publish twice and separately for thises two sets of devices....or is the software intiuitive enough to know the difference if you publish once?  I am asking because I have them published separately now and publishing to HTML5 has quirks with the menu and navigation. I dont want these quirks to effect those using their regular old computer/laptops... 

So Do I publish twice for the 2 types of computers or is the software intuitive enough to know the diffence and I can publish once and click output to HTML 5 when publishing taking care of both modes of delivery?