The software evaluates your database to see what's needed, and automatically checks the boxes for the steps that it knows need to be done.
If in doubt, clicking the "Recheck" button will re-scan and see what's needed.

In almost all cases you should never normally need to check a box that isn't automatically checked. They're made available for ease of troubleshooting if it were necessary, but those unchecked boxes are really not intended to be used unless you have very acute knowledge of the what and why behind each.