Yeah, I never understood that phrase either, because you’re right: your head is kind of always above your heels.
And another thing I realized yesterday: people know that Asia is the “East,” and Europe is the “West,” but take a peek at their relation to the North American continent… the “East” is to the west, and the “West” is to the east. I know they were named in relation to Europe, but it’s fun to think about!
(Sorry, I just had to point that out)

The phrase originated in the 14th century as ‘heels over head’, meaning doing a cartwheel or somersault.’Head over heels’ is now most often used as part of ‘head over heels in love’. When first coined it wasn’t used that way though and referred exclusively to being temporarily the wrong way up. It is one of many similar phrases that we use to describe things that are not in their usual state – ‘upside-down’, ‘topsy-turvy’.

Not to dissuade a more creative answer, but the phrase was originally “heels over head,” but “head over heels,” is easier to say even though it makes no literal sense. The original wording makes sense in context, as you’ve fallen (i.e. heels over head) in love.
Here’s more info for you:
http://www.phrases.org.uk/meanings/head-over-heels.html

Apparently I’m a little too slow.