Much of an application's crypto configuration and potential flaws can be identified and verified simply through connecting to the application and seeing what was negotiated. This can be pretty labor-intensive, so luckily we have some fast scanning tools that will systematically negotiate all potential configurations from a server to better help us understand what they are allowing.
I would still recommend spending some quality time learning how to test SSL/TLS manually, as it is always handy to have a quick check to ensure versions, cipher preference, and similar ones. A great writeup and cheatsheet is available at http://www.exploresecurity.com/wp-content/uploads/custom/SSL_manual_cheatsheet.html.
