You apply the SSL certificate to the entire website and just enable it in nopCommerce. The site will automatically switch to https when it needs to (checkout). It's pretty simple.
You can get cheaper SSL certs at GoDaddy.com that you can then install on other hosts. (Though I would not recommend hosting on GoDaddy with their low cost shared plan.) You will have to do a little more work compared to having the hosting company use their own cert (e.g. generate CSR, copy files, etc).
Also note, that I think there is still an issue will SSl on nopC - once you've gone to a page that is secure (https://), then all subsequent pages in your session will be secure. For example, even if you go to the register page, and don't register, and click Home link. This has been discussed in forum before - even just today https://www.nopcommerce.com/boards/t/15946/ssl-setup-and-links-back-to-non-secure-pages.aspx