in the q3.game directory should be a baseq3 directory, a missionpack directory, a default build_build_menu.xml, and a game.xlink
in both of the above mentioned directories should be a default_shaderlist.txt and an entities.ent file
make a copy of the q3.game directory and rename it to oa.game
go into oa.game and rename baseq3 to baseoa
go into both baseoa and missionpack and replace both of the default_shaderlist.txt files with the attached default_shaderlist.txt file
start up gtkr
choose open arena from the drop down list and enter the path to the engine when it asks.
then after startup go to edit > preferences > paths and make sure that you have the correct path to the engine setup.
The build menu:
bsp is just the meta stage
vis is the vis stage
light is the light stage
All three should be used in a final map, though you may not want to use the default options, visit here: http://en.wikibooks.org/wiki/Q3Map2
for the full list of command switches ) note our engine supports flares so be sure to add -flares to the bsp stage of the compile though it is out of date (the latest and probably last version is 2.5.17 and there are a few switches that aren't documented there).