You have two options :
1)Use Worldbuilder to add/remove civs.
2)Open the WorldBuilderSave file in Notepad (or the text editor of your choice). It is just a text file with a special file extension.
There are several sections :
First, a section the has some special settings
Code:
BeginGame
Speed=GAMESPEED_NORMAL
Calendar=CALENDAR_DEFAULT
ForceControl=FORCECONTROL_SPEED
GameTurn=160
StartYear=-4000
Description=TXT_KEY_MAP_DESC_EARTH1000AD
EndGame
Then, you get the Team listings. Between "BeginTeam" and "EndTeam", the team gets a list of Technologies (Tech=TECH_MINING), which teams they are at war with (AtWar=10),anyone they have Open Boders with (OpenBordersWithTeam=5), etc..
After that you get the individual Players, each between a BeginPlayer/EndPlayer pair. It has waht team they are on, who they are, the leader, starting civics, starting money, etc.
Finally, there is a listing of each plot on the map. Location, terrain type, any units present, improvements, cities (and what buildings and religions are in said city), AND which teams have seen the plot (and therefore know its initial condition).
Personally, I would use WB...