1. Your season pass does work at SFNE. If you have the Gold pass you will have free parking. If not, be prepared to pay either $25 for regular, $30 (I believe) for preferred parking, or $5-$10 for parking at a bunch of lots that line the street.
2. If you are going in September, then lines should not be too bad as it's a slow time for parks in general, as well as there is the Big E about 20 mins away and that will draw most of the crowds. Beware of traffic jams that may be caused from the Big E though. If you want to ride Wicked Cyclone a lot, be advised that it is only on the Platinum Flash Pass (about $90), not the other two versions.
3. My advice would be to join the rush and go to Wicked Cyclone and New England Sky Screamer first. They are two of the most popular attractions, NESS's line moves slow due to capacity, so get it out of the way early. WC will consistently be around 35-45 mins throughout the day, avoid it during the peak 12pm-4pm hours though as it can get to over an hour. Pandemonium is also near those two rides and gets a big line fast, so do that third. Bizarro is the other top ride, but with two trains the line won't get too bad as long as it's not a Saturday in mid-late October.
Other popular rides are Scream, Goliath, Thunderbolt, Batman, and the Bumper Cars. Personally, I would wait to ride those until a little later in the day, once the crowds die down. If you go back for a second day, try doing Bizarro first, in the front row, before it gets the additional 30 min front row wait.
SFNE is a much compact feeling park than Great Adventure, but provides a lot of thrills. Have fun!
