Eventually I hope to have a step by step full installation guide for Microsoft SQL Server in this wiki, however, until this happens I recommend you perform a default install of the product and then configure it so that you meet the following conditions.
1) Create a new empty database for Commander4j - you may find it beneficial to create several, i.e Commander4j_Test, Commander4j_Training, Commander4_Live etc
2) Ensure that the database will permit TCP/IP connections.
3) Ensure that the database will accept both SQL Server Authentication and Windows Authentication.
4) Create 1 user per database for Commander4j to use. Recommend full permissions.
5) Associate the user with the appropriate database, i.e. User cmd4j_test has a default database of Commander4j_Test and so on....
6) Test each user and database using SQL Management Console to validate that the account is working properly.
7) If you want to run the application on remote PC's connected to a central database also check that the firewall of the database server will permit remote TCP/IP connections.