once you have flex open, just go to the 2nd tab at the bottom (labelled cloud) and scroll till you find "Springboard"
From there scroll till you find "Notification Center - Disable" and tap the upper right glyph (cloud with arrow).
Go back to your patches tab (first tab at the bottom) and enable the patch by highlighting the check mark.
Flex will ask to respring. Do it and it should take effect (respringing is only required for springboard patches).
This is all assuming you have a purchased version of flex 2.
not too sure about SwipeNav. Are you on iOS 6 by any chance?