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I have a website that I'd like to track properly with Google Analytic. The main site is just MySiteExample.com. There is also a store setup so we are using https on part of the site. My question is do I create different profiles for each variation of the domain name? If yes, do I embed all 4 of them one after another?
URL Variations:
MySiteExample.comwww.MySiteExample.comhttps://MySiteExample.comhttps://www.MySiteExample.com
If you look at the example JS code at the Google Analytics help, it does not matter whether e.g. index.html is served through http://www.mysiteexample.com/index.html or https://www.mysiteexample.com/index.html, as both will trigger the same tracking event. If you serve different content depending on whether the protocol is https or not (i.e. two different index.html, if we stick to my example), see this question.
Without a good reason you should not serve exactly the same site at http://mysiteexample.com/ and http://www.mysiteexample.com/. That makes SEO worse, messes up bookmarks and links etc. Decide if you want to serve the site from www or not, and set up a redirect for the other version. See e.g. this question for details how to do this on the Apache web server.
www. They are called "Unique Resource Locators", and uniqueness is not having two different URLs pointing at the same resource...
You can use 301 redirects & Canonical Meta tags to address the issue here.
Select the url scheme you want to follow & then apply 301 redirects to other type of urls. This way your page ranking & weight will be preserved.