If some of your learners will be accessing your course on a computer and others will be accessing your course via iPad and the course contains assessment screens, you will need to have 2 different versions of the course if people will be using IE9 or earlier. (If there are no assessment screens in your course, only one version of the course would be required and that would need to be the iPad compatible, or HTML5 version.)
When creating a course, the default setting is Flash. To make the course available in both formats, start by making a copy the course. Then set one of the courses to be iPad compatible, by clicking on the “convert” button.