I just bought a '99 Scrambler 500 4X4 and don't see a dipstick like on my Sportsman 400.

 

Take off the plastic cover on the right side where your foot brake is. You will see the 9/16" bolt on the tranny, similar to your front 4x4 gearbox. Unscrew that bolt and the way I understand the manual, the fluid should be 1-5/8" below the top of the hole. I just make sure I see fluid and that it doesn't have water in it.
Enjoy your Scrambler, it's one awesome 4x4.