Yes screw the 2 in further to bring the block (trem) down. If you want to use the trem though that will always happen. (some what)
Detune the guitar first then screw them in a bit ,tune up and bend some , repeat the procudure till it stops moving . I have mine so they are flush will the body all the time. Do not burry the screws (ie. don't overtighten) in the body, could crack the wood. If you have any doubts on working on it yourself take it back in and have the repair guy setup the guitar to play to your liking.
http://www.fender.com/support/stratocaster.php setup for using trem