What is the function of the Save button on the interface?
It's to save your progress. Normally when your in the middle of doing one of the sections you may decide to come off the computer and do something else for a while well if you hit the submit button it will save your work but also provide you with an error “if you didn't complete the section”.
Where do I put the Save button?
Putting the 'save and exit' button above the primary button implies it's more important, when it isn't. Putting it below can cause an unwieldy list of stacked buttons and uses the area reserved for the cancel button.