I use everything, with some randomization to determine what gets used in any given game specifically.
1. Determine Inner Region: Roll a die. On a 1-2 result, do not use the Dragon board overlay. On a 3-4 result, place the Dragon Tower side face-up over the main board as the Inner Region. On a 5-6 result, place the Dragon Realm side face-up over the main board as the Inner Region.
2. Determine Ending: Roll a die to determine if the ending will be Revealed or Hidden. On a 1-3 roll the Ending is Hidden. On a 4-6 roll the ending is Revealed. After rolling, remove the unused Hidden or Revealed Ending cards from the Ending deck and shuffle the deck. Draw one Ending card and place it on the Crown of Command space. Face-down if Hidden, face-up if Revealed.
Note: If the ending is the Dragon King, ignore the rules on the card and instead follow the rules for which Dragon is King using the Dragon expansion ending rules.
3. Determine Omen deck: Lay out the four stacks of Omen cards and roll a die to select which stack will be used. Use 1-4 from left to right, re-rolling 5 and 6. Collect all eight Omen cards belonging to the selected Omen set. Then use them to make a face-up stack, starting with the 7th Omen at the bottom, then the 6th Omen, 5th Omen, etc., with the Prophecy card on the top. The stack is then placed next to the Harbinger sheet.
4. Cataclysm: There are Seven Omen cards, plus the beginning Prophecy. When the Omens advance, roll a D6. Add the number of the new Omen to the roll. On a 6+, the Cataclysm has arrived! Discard all face-up cards on the main board. Replace the main board with the Cataclysm board, placing Characters, the Grim Reaper, the Werewolf, and the Harbinger on the same spaces they were previously in. Place Remnant cards on spaces with a Remnant symbol as the Cataclysm setup rules dictate.
To keep play moving smoothly, I randomly draw the dragon tokens for each player instead of passing the bag around. It just seems to work better if one player "GM's" the game. If you have all experienced Talisman players that are all actively paying attention and people want to draw their own tokens, sure, go for it. That's rarely the case for me though. Same goes for cards, I typically have all the cards in one bank area next to me and draw and hand over cards from the appropriate stacks. Experienced players will grab cards if they want, ones that aren't so comfortable with what's going on don't have to deal with remembering what stack to grab from, I just hand it to them.
Honestly the game plays as smoothly with every expansion as it does just the base game this way. I'm the only one that has to keep track of the complexities, and since I'm the game owner for my group and have the most experience with it (especially after creating and publishing the all in one rulebook ), that's no problem.