The BizTalk Server Best Practices Analyser  allows you to carry out a configuration level verification of your BizTalk installation, evaluating the deployed configuration but not modifying or tuning anything that it finds. The Best Practices Analyser uses "reading and reporting" to gather data from different sources, such as:

• Windows Management Instrumentation (WMI) classes
• SQL Server databases
• Registry entries

When I first ran the analyser I got a number of errors, if you get any errors these should all be acted upon to resolve them, you should then run the scan again and see if any thing else is reported that needs acting upon.

As you can see in the image above, the initial issue that jumped out to me was that the SQL Server Agent was not started.

The reasons for this was absent mindedness - this run was against my development PC and I don't have SQL/BizTalk actively running unless I am using them.  Starting the agent service and running the scan again gave me the following results:

This resolved most of the issues for me, but next major issue to look at was that there was no tracking host running. 

You can also see that I was still getting an error with two of the SQL jobs.  The problem here was that I had not yet configured these two SQL jobs.  Configuring the backup and purge jobs and then starting the tracking host before running the scan again gave:

This had cleared all the critical issues, but I did stil have a number of warnings.  For example on this report I was warned that the BizTalk Message box is hosted on the BizTalk Server.  While this is known to be less than ideal, it is as I expected on my development environment where I have installed Visual Studio, SQL and BizTalk on my laptop and I was happy to ignore this and other similar warnings.

In your case you should take a look at any warnings you receive and decide what you want to do about each of them in turn.