Cpanel acts as a front-end to the apache configuration file httpd.conf. It builds this base file and that file will include other files at various "levels" if those files exist.
Cpanel by default accepts only 1 SSL cert per cpanel account and by default this is applied to the primary domain name associated with the cpanel account.
If your storefronts are in a subdirectory of your main domain (foo.com/subdirectory) then the one main certificate will work for those domains.
If it's a wildcard certificate, you can apply that certificate to the subdomains of the main domain (sub1.main_domain.com, sub2.main_domain.com).
If it's a multi-site certificate, then you can assign that certificate to the parked/addon domains you have configured for your store.(foo.come, bar.com, etc.com).
If you want to use individual certificates for each storefront then you have to use the cpanel include files for each specific domain that will point to the SSL certificate FILE related to that domain. It is possible to use but is a manual setup. Your hosting might be able to help you if you get beyond the tier-1 support.
Single site certs are cheap to free. Wildcards are more expensive and multi-site certificates are the most expensive. So you can trade $$ for time/risk/experience. Note that cpanel is not usually very good about maintaining some of this stuff when it upgrades. So risk to your business of doing any manual configuration using cpanel extensions is higher than simply using a wildcard/multi-site certificate.