Which set of instructions are you following? LTC uses the Kingdoms exe but it's not a Kingdoms mod per se. In Kingdoms you can start a hotseat in the game menu.
Most likely you'll have to follow the instructions for vanilla MTW2. In that case after you make the changes and switch the preferences file back to read only you cross your fingers and start up the game. You should be able to click on multiple factions once on the campaign screen.
Note there is also a trick that allows you to fight defensive battles in hotseats that would be needed for the game. It was used for both LOTR and KOTF, but it's been so long I don't remember how it was done...
Edit: That was surprisingly easy to find. For defensive battles. I'll see if it works for me in a few.
http://www.twcenter.net/forums/showthread.php?t=288683
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