Actually, I believe that both methods of carrying the Greatcoat/Blanket are mentioned in the 1861 (Revised) regulations. When this site first went up ('99/'00? Before the great crashes), there was a copy of them, and some Quartermaster/Commissary documents in the articles section that when read together made all of this completely clear.
In the original version of the regs (actually written a year or so before the war, and not effective until 1861), the blanket is folded in the knapsack and the coat goes on top. The rest of the bag is filled with whatever the Pre-War Army thought a Soldier needed to carry. The dog tent and gum blanket had not yet been adopted. This was fine and good for the times. The Army wasn't actually going any where, so when it moved, it moved at the pace of it's wagons.
War starts. Now, the Army must move, fast. The Army imediately realizes that it's logistics system is inadequate for the task. The LOG Train can not keep up with the Combat Army.
Details, the haversack will only hold three days marching rations and mess furniture. Been tried by folks on this forum. Cartridge box will only hold fourty rounds (.58 cal musket with tins). Not enough to sustain a Soldier in the field while waiting for supplies.
The Quartermaster Department issues orders that the new basic load of each Soldier is to be increased to five days rations and eighty rounds. This is almost imediately followed with a revision to eight days rations and 120 rounds of ammunition. (all of this is in theroy of course, we know that the Army was hard pressed to supply the original ammounts). Where is the Soldier going to carry all this extra?
The "Revision" to the regs then says that the Blanket is to be rolled and carried on top of the knapsack, and the coat (if carried) should be folded and placed between the folded sections of the bag. The bag was not emptied to make room for more socks, shirts, uniforms, books and what not, but for the stuff a Combat Soldier needed to stay in the field, food and ammo. Most Soldiers were already doing the "Lighten the Load" to what was needed any way.
The problem is that all of this info is tucked away in the little "nooks and crannies" of 19th century Army instructions, painful reading for me. But it's all there. It might even still be on this site somewhere. I haven't figured out how to make the spell check work yet, so I have no luck searching for stuff any more.