Okay you gotta find the folder you saved the map too, most likely it will be under documents, in 'my games' and a civ folder of some kind, under 'saves' and then 'worldbuilder'. You should see the map there unless you saved it somewhere else.
In order to remove existing civilizations you gotta open the map in Notepad. Most of the map is saved in this. When ever you want to allow user picked civilizations you gotta go here.
At the top should be lines talking about map info and teams techs, ignore those, but scroll down and you should see player info after teams, looking sorta like this:
BeginPlayer
LeaderType=LEADER_HATSHEPSUT
CivType=CIVILIZATION_EGYPT
Team=0
PlayableCiv=1
StartingX=69, StartingY=37
Handicap=HANDICAP_NOBLE
EndPlayer
or more likely
BeginPlayer
Team=0
LeaderType=LEADER_CATHERINE
LeaderName=Catherine
CivDesc=Russian Empire
CivShortDesc=TXT_KEY_CIV_RUSSIA_SHORT_DESC
CivAdjective=TXT_KEY_CIV_RUSSIA_ADJECTIVE
FlagDecal=Art/Interface/TeamColor/FlagDECAL_DoubleEagle.dds
WhiteFlag=0
CivType=CIVILIZATION_RUSSIA
Color=PLAYERCOLOR_DARK_RED
ArtStyle=ARTSTYLE_EUROPEAN
PlayableCiv=1
MinorNationStatus=0
StartingGold=0
StartingX=89, StartingY=71
StateReligion=
StartingEra=ERA_ANCIENT
RandomStartLocation=false
CivicOption=CIVICOPTION_GOVERNMENT, Civic=CIVIC_DESPOTISM
CivicOption=CIVICOPTION_LEGAL, Civic=CIVIC_BARBARISM
CivicOption=CIVICOPTION_LABOR, Civic=CIVIC_TRIBALISM
CivicOption=CIVICOPTION_ECONOMY, Civic=CIVIC_DECENTRALIZATION
CivicOption=CIVICOPTION_RELIGION, Civic=CIVIC_PAGANISM
Handicap=HANDICAP_NOBLE
EndPlayer
Your going to need to paste over this so it looks like this instead for each player. Just copy the bold part below and paste it over everything from leadertype to handicap. Just be careful to make sure teams remain unchanged (teams 0 thur 17). Just be careful, you might want to practice on another map first so you don't ruin one you worked on. You'll have to make sure all civilizations look like the blank one below or else the game will force you to choose one of the preset ones.
BeginPlayer
Team=0
LeaderType=NONE
CivType=NONE
Color=NONE
ArtStyle=NONE
Handicap=HANDICAP_NOBLE
EndPlayer
I can't help you much with start locations, the game assigns them and my efforts to try and control them ruin the map file.
Hope I managed to help you.