When I started up a game, I had some civs close together so they knew each other from the start. I opened WB (I was trying to make a completely different scenario so the start game didn't matter at all) and moved all the civs around and unrevealed everyone's tiles except those in the capital. However, some civs still are in contact with each other.

Here's my problem: I can't figure out how to make civs not know each other from the start.

In my scenario, Bismarck is in contact with Pacal II and Qin even though Bismarck has no line of sight in their territory or units and the same goes for Pacal and Qin. Each of those three are actually on their own continent so that's quite a distance.

Save the WB file and open it with a word processor. When you do, you'll see something like this for each team (player):
BeginTeam
TeamID=1
Tech=TECH_MYSTICISM
Tech=TECH_MEDITATION
Tech=TECH_FISHING
Tech=TECH_THE_WHEEL
Tech=TECH_AGRICULTURE
Tech=TECH_POTTERY
Tech=TECH_SAILING
Tech=TECH_HUNTING
Tech=TECH_MINING
Tech=TECH_ARCHERY
Tech=TECH_MASONRY
Tech=TECH_ANIMAL_HUSBANDRY
Tech=TECH_BRONZE_WORKING
EspionageTeam=0, EspionageAmount=172
EspionageTeam=2, EspionageAmount=153
EspionageTeam=4, EspionageAmount=55
EspionageTeam=5, EspionageAmount=306
EspionageEverAmount=702
ContactWithTeam=0
ContactWithTeam=1
ContactWithTeam=2
ContactWithTeam=4
ContactWithTeam=5
AtWar=0
RevealMap=0
EndTeam

You scroll down the document to find out which team is which and then delete the line. Say you don't want team 1 to have contact with team 2, you delete ContactWithTeam=2 in team 1's definitions and ContactWithTeam=1 in team 2's definitions.

Thanks! :)

Just curious, but what is this EverEspionage value I found in the WB file?

I'm not sure, but I think it's the total espionage spending throughout the game.