Best Practice #1
Before you start upgrading BizTalk360 to the latest version, you always take a backup of the 'BizTalk360' database. This is just a best practice and it will come handy if something goes wrong and you want to roll back to the previous version.
Best Practice #2
BizTalk360 allows you to configure and manage multiple BizTalk environments (Production, SIT, UAT, etc) from a single place with one instance of BizTalk360. As a best practice, we recommend customers not to add all the BizTalk environments to single instance and instead group them logically. Example: Production/Disaster Recovery can be in one instance. Important QA environments like Staging/UAT can be in one instance, and non-important environments like Development testing, Integration testing etc can be in another.
BizTalk360 is designed as a central monitoring solution, rather than agent based solution. There are pros and cons in having a central monitoring solution. One of the great advantage of having a central monitoring solution is that you do not need to install any additional agents in your important servers, and also it avoid the whole complexity of managing the agents, agents doing duplicate work etc. On the negative side, you need to watch out for scalability. The way we scale BizTalk360 is by installing multiple instances of BizTalk360 for different environments. Hence it's also important you do not add all your available BizTalk environments to a single installation of BizTalk360.