There are several settings you change in the Preferences Window. Make sure you press "Save" to save your changes or "Revert" to discard them.
Flagged Functions let you set up your own columns that perform searches for you. You maintain the current set of flagged functions on the Flagged Functions panel. You can restore the default flagged functions that shipped with FMPerception by clicking Restore Function Defaults.
There are several different ways you can view the hierarchy of elements in your FileMaker system. You can set which one you are using here. "Column Style" is probably most familiar to Mac users. "Outline Style" is closer to what a Windows user might expect.
It's helpful if we can collect some information about version updates and crashes. You can opt out of this by unchecking the boxes on this panel.