It's entirely possible your package tray was hacked by a PO, otherwise they wouldn't fit trying to stuff a 6x9 into the opening from the top side. The 6x9's gotta go under the package tray and the screws would go in from the top side. Several owners have found this out the hard way
Well unless your 6x9's were really 6x8's, then I could see them fitting from the top side...