You applying certificate to the website.
Also please pay attention that certificate is valid for full website name.
If you bought it for
www.mysite.com then IE ( or any other browser) will give a warning message if someone will try access
https://mysite.com (notice no www)
There are more expensive versions of certificates that work with domain and any subdomain. (ie if it valid for mysite.com then it's valid for mydomain.mysite.com.
You then on server set the setting that this folder or file requires SSL.
Also all links to those pages or folders should be in format
https://www.mysite.com/protectedpage.html
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So the answer to your question is yes. You can (and i say should) protect only subfolder or pages that have customer information.