There are three bolts in the top hinge and three in the bottom hinge, both on the car side of the hinge. A couple of them are accessible through the front wheel well with the liner removed, the rest are accessible with the kickpanels removed from the interior.
If the doors have never been off, chances are your hinges are just sagging. A search should find a ton of threads with solutions.
Its been a while since ive done it but if I remember correctly, remove the middle bolt from the upper and lower hinges, have a buddy or a jack (i used a jack) hold the door up at the end with a little pressure. Barely loosen the remaining 4 bolts and lift the door just a little. Tighten the bolts and carefully close the door. Keep repeating this till its where you want it. The 2 bolts you took out more than likely are not going to go back in cause the counter bore in the hinge is only big enough for the bolt to pass through. I did this a year ago and I havent had any problems with the doors since I did it. Although it isnt reccomended to leave out bolts I did it with very good results. U can go as far as making the hole bigger to allow for the adjustment. Its very good if your on a budget