The first few times I played the game I've placed the cards in the rooms in the order that the Seed Cards reference tells me to, but I find that some cards at the bottom of each pile are supposed to be there to "unlock" access to the rest of the stacked cards within that room. Can I change the order each stack is placed on the board so it makes sense or do I need to follow the reference sheet which I find is wrong?
Ah, I struggled with this as well. The order in the manual is the order in which you lay the cards down, so the card at the end of the list is the card that ends up on top.
So the exploration cards will always be under the obstacles/locks, and in the rare case where a room contains an obstacle and a lock, the lock will always be on top of the obstacle.
Also, equipment and clues are always on top of "nothing of interest" cards.
No, you cannot change the order of the Seed cards. However, do make sure that you are using the latest errata.
If you have any specific concerns, please ask. We can try to address this question without specifics.