You can define several parameters in AllMyPDFs. Please chose this menu item in order to open the settings dialog. It offers various tab views:
Here you can define whether AllMyPDFs should be automatically launched when you start your computer.
If you check this option, the document area will be darkened when a sheet drops out of the title bar / toolbar. This increases the focus on the sheet.
Here you can define how PDFs will be presentated by default. The options are self-descriptive.
Define or adjust the highlight color which will then highlight any places which fit to your search term when you search inside a single PDF (using the Search Inspector).