wmorris:
Well, according to google some or most pages fail because of this "Alternate page with proper canonical tag". How can I fix this?
Making sure your SSL, and your ultimate URL match should take care of it.
If your SSL is set for https://www.yoursite.com, all URLs should be redirected to wind up at https://www.yoursite.com.
A 301 can be done in cPanel or equivalent controllers or added to your root's .htaccess file.
All e-commerce sites should be forced to https://. That can be done in cPanel or .htaccess as well. Of course, both configure.php files should be set for https:// as well.
Google and other SEs look at the following sites as duplicates:
https://www.yoursite.com
yoursite.com
test.yoursite.com (if the same data from your main site is located there for testing)
There are ways of letting Google and the other SEs know that test.yoursite.com is not a duplicate but that's another story.