it depends on how bad you want them mounted flush. if you don't mind a little cutting, then do this.
take the seat back out. remove the 3rd brake light and the rear deck. take a pair of tin snips and get ready to make three cuts. one is on the little skinny piece in the middle. the other two cuts are vertical and about 6~7"s apart. what that allows is the body of the 6X9 to protrude into the back seat area about 1/2". don't worry, the seat will go back on fine. get a couple of drywall screws and shoot them through the sheet metal. then, take a pair of pliers and break the screws off. (they're hardened, so they'll break off flush). don't put your eye out either! when the package tray is reinstalled, the install looks stock.
unless the speakers have HUGE magnets, they will clear the trunk rods. there might be some rubbing, but i've never seen a problem from that. if the rods touch, there's enough spring preload to prevent any buzzing.
don't worry, it's easier than it sounds. just look at the tray and the speaker and you can see what needs to be done.
if the idea of taking the snips to your car makes your midsection queesy, just ignore all the horrible images i just tried to conjure.
earl