I want to play the Mission Paks with a source port, particularly KM Quake. How do I go about loading it into the sourceport?

I don't have the mission packs, so I'm just taking this information from sites I found online.

Go to the official KMQuake download site:
http://www.markshan.com/knightmare/

Download this file:
Official mission pack support (also needed for Pax Imperia):

Install that on top of KMQuake.

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I don't use KMQuake, so I don't know if it will let you select the mission packs after starting the game. An option though is to create a batch file that should let you chose.

A batch file is just a text file with the extension .bat (instead of .txt). It's a plain text file.

I found this guide online:
I've found a solution, but it isn't an elegant one. Basically, create a quake2.bat file with the following text, and it should help you with playing the expansions. (put it in your quake 2 installation directory. You can create a desktop shortcut to the batch file if you want).

@echo off
echo Quake II + expansions
echo 1: Quake II
echo 2: Mission Pack 1: The Reckoning
echo 3: Mission Pack 2: Ground Zero
set /p userinp=choose a number (1-3):
goto %userinp%
:1
goto end
:2
set game%=xatrix
goto end
:3
set game%=rogue
goto end
:end
kmquake2.exe +set game %game%

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Or, you can create separate batch files:
quake2-reckoning.bat
contains:
kmquake2.exe +set game xatrix
-
other batch file:
quake2-groundzero.bat
contains:
kmquake2.exe +set game rogue

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Again, I haven't tested that but it should work.