The site that gets the SSL must be the one you assign a unique IP to, which is required for SSL. So, you just need to pick which domain you want that to be, then proceed from there.
If you have any worries about duplicate content penalties with the search engines, you could change the mirrored domains to redirects.
Also, note that www or non-www matters as well, so be sure to pick the ones you want to stick with (www.example.com or example.com) -- or any other subdomain, like secure.example.com.
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