I have this working now on a zen cart install and wanted to make it work for my new store on Magento.
Now I have a ssl cert installed on my primarydomain.com.
I have my store in a add on domain and it can be seen either at addondomain.com or primarrydomain.com/addondomain/
In Zencart I can use https://primarydomain.com/addondomain/ and my site works fine and is under the ssl cert.
I can set it up in Magento using configuration/web and go to secure and enter the url but it does not work because the path is not there on a link going to my Account or login.
Is there another way to make Magento use paths that are correct. I am sure that index.php is getting the path and converting it to the correct one in code.
It sounds like you're going about it the right way. You need to update your configuration details or the secure url section: http://docs.magento.com/m1/ce/user_guide/configuration/url-secure-unsecure.html
You will then need to flush all caches and refresh the page, and the changes should take effect.
ssl certificate must be issued for top-level domain.
for addondomain.com or primarydomain.com
then you can see either one
and you base url must be exactly the same as you type it in browser.