I've been reading everyone's comments on this post with great interest. I'm now in the process of creating my own 4th Edition campaign/Adventure Path and I've run into the Room No./Encounter No./Treasure Parcel bookkeeping situation myself and it presents a real problem.
I'm going to ramble a bit here so please feel free to skip down to my solution if desired! :lol:
The motivation behind separate Encounter Pages away from the main dungeon was, I think, to keep all things combat in one place. It works for that but leads to a problem of having room regions and combats on different pages with potentially different numbering systems.
The Treasure Parcel system was designed so that a GM could tailor make treasure suited for their parties rather than dish out yet another +1 Halberd that no one uses. The problem here is that the treasure parcels are listed in a separate place from the room description which is in a separate place from the encounter description.
So, here is what I'm doing for my new campaign and I would appreciate any thoughts, pro or con as long as they are moderately polite!
I am numbering my encounters 001, 002a, 002b, 003, etc.
I number my treasure parcels to correspond with this when treasure is associated with a combat. Treasure Parcel 002a goes with Encounter 002a.
I DO NOT number my rooms. I name them. Kitchen, Dining Room, Kennel, etc on the map but I do also place the Encounter Number in the rooms where there is an encounter. On the GM map it will show "Kitchen (Enc 002a)", "Dining Room (Enc 003)", etc.
I alphabetically place room descriptions in the Adventure on a level by level basis. All level one room descriptions come after the level one map, etc.
Any treasure not associated with a combat goes directly in the room description associated with the room name, ie. "Pantry - 10 jars of grape jelly (2 silver per jar)".
Oh, and finally, about the 002a and 002b. I found that I was creating a number of optional encounters based on Skill Challenges (I have a non-WotC system there as well) that the group might or might not encounter. So if they are going to fight the Monster but might encounter another monster on the way because of a failed skill challenge the two encounters become 002a and 002b. Also, 002b gives no experience as it is the result of a failed Skill Challenge.
Anyway, I've gone on too long but, needless to say, I agree with most of the complaints about the way WotC has handled their organization with the modules.