I had a season pass processed at another Six Flags park last year, and when I went to Great Adventure, all I had to do was flash it and they let me walk right in.
I recommend you go to Batman the Ride first, it usually has the longest lines, then head right next door to The Chiller, fallowed by Skull Mountain, this way you're not walking in circles. Then go over to Medusa (not too long a line either) and then to Viper which is right through the woods. Rolling Thunder and Scream Machine never have too long a line, if they have a line, but The Log Flume, and Stuntman's FreeFall usually have very long lines (depending on the day) so hit those early. Also, if it is opporational, Escape from Dino Island 3D may have a really long line, but it is more than worth the wait. Basically, the best way to cruise the park is start from the right side and hit all the coasters going in a circle to the left, then go through again hitting all the other rides. It will save you tons of time.