Hi I'm quite capable of getting these rules wrong especially with so many double negatives and the baggage rules have got quite complicated, so here goes.
As I understand it Army baggage has to be held in a separate Command with a min of 4 elements, which doesnt have a PIP dice (see page 9). As this command used to be called Train I retained the name for familiarity. Again see page 14 other elements can be included in this command hence the need for a 5th column.
To input baggage you should the following:
Army Baggage needs to be entered in the first 2 Army Baggage rows against the contributing command A - D (most lists have options for baggage in camp or wagons/cart, hence 2 lines in case you want to specify/take both) This will then tally the ME in both the contributing command and the train command which contribute to the army total. (see page 42).
Command baggage should only be entered in columns A - D according to which general it belongs to. This tallies the ME only for that command (see page 42).
Best way to see how it works is to clear all the commands and just enter 1 baggage element against army baggage and then repeat but for command baggage.
Hope this helps