Grant Fritchey (5/7/2014)

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Not sure about the encryption. I'm not sure why that would affect performance much at all (a little in the CPU I suppose).

As to figuring out how the server is running, there are a ton of tools built into SQL Server. First, and most important, are the dynamic management views (DMV). The very first one of those you'd start with to understand why or how a system is running slow is sys.dm_os_wait_stats. That will show you what the server is waiting on. You can also use the DMVs to look at currently existing queries (sys.dm_exec_requests) an aggregation of query performance for queries in cache (sys.dm_exec_query_stats) and others. There's a book on this (free download e-book) by Tim Ford and Louis Davidson.

Another tool is to run perfmon to capture performance monitor metrics. This will let you capture general behavior and load indicators such as cpu percentage, memory use, and others.

After that, you start to get into more specialized tools such as extended events to capture certain types of behavior or events such as query execution time and other things.

There's a lot to this. In fact, the first several pages of my book (in the signature below) are all about capturing system behaviors in order to understand where your system is running slow.