What do the options do?
Selecting "Start Fraps minimized" will hide the Fraps dialog screen when you launch the program. Fraps can still be accessed through the icon in the system tray.
Selecting "Fraps window always on top" will ensure the program window remains visible even when switching to another application. This option has no effect if Fraps has been minimized to the system tray.
If you'd like Fraps to be loaded when you turn on your machine enable the "Run Fraps when Windows starts" option.
Fraps also supports separate LCD screens on keyboards such as the Logitech® G15™. If you have a supported keyboard you will see the option to "Display status on keyboard LCD". Enabling this option will allow you to see FPS graphs and other identifiers on the keyboard while playing your games. If you have a G15 but do not see this option then you may need to install the latest G15 drivers available from Logitech's website.