Once you have managed your latest domain's DNS settings so that their status on your Shopify admin's domain page is "OK" then when an SSL certificate(s) become available you will be given the option to activate it. You should not need to keep checking your domain page either since a notice will appear on your admin's homepage once ready. :)
In the meantime if you are concerned about customers shopping on the site before the SSL is ready I would suggest setting a domain that it has already been provided one for as the primary.
Keep in mind that the storefront SSL is still a relatively new feature (unveiled in Feb 2016) and your site is still secure based on the security measures in place before this addition. All checkouts are completed on an SSL-protected domain "checkout.shopify.com". All payment information stays within that SSL protected domain and is not transferred to your website. So, rest assured, your customers' sensitive data is safe and secure.