You have a bunch of different questions in here.
Q: What is the "Always On" thing?
Microsoft uses that brand name (which was written without a space before 2016) to describe two different features:
- Failover Clustered Instances (FCIs) - what your grandpa used to call an active/passive cluster
- Availability Groups (AGs) - like database mirroring, but works with groups of databases in some cases (but not the system databases)
Use those terms to describe which specific Always On feature you're using.
Q: In a failover, will it be always on?
Neither FCIs nor AGs are really always on. During a failover, your running transactions will fail, and connection retries can fail for 5-60 seconds (or more). It's up to you to build in graceful retry logic in your applications, or build in degraded capability tools like Stack Overflow does.
Q: How do I configure Always On?
It varies dramatically based on:
- Which AO feature you're using (FCIs or AGs)
- The number of nodes in the cluster
- How you want to handle quorum (voting)
- Whether you're using automatic failover via a listener or virtual computer name
These are big decisions that involve a lot of architecture work. For more detailed specifics, include the above details, and we'll be able to tell you more about how to configure it.
Q: Isn't it just a matter of checking the box for Always On?