Hi Frenchdoor,
I think your order was a little incomplete.

First off, 6S on your motor should be fine, but expect it to run fast (Are you sure you didn't get the 500kv motor?)

Anyway, You should have gotten 2 female (For the batteries) EC3 plugs and 1 male (For the ESC). If you got any instructions on the EC3, use that. In order to run them in Series, you may be able to buy an EC3 series connector from your LHS. Your motor will have the 3 bullet connectors already installed on it. You need to find the mates in the package and solder them to the three red ESC wires. You will then plug them in and shrink wrap over them individually. You don't need to shrink the EC3 connectors on the battery if they are soldered properly.

When I placed my order I ordered a couple of sets of the Turnigy 4mm connectors (red). They are both male and female together and you just need to make sure you setup the connectors on the correct wire.
Good luck and PM me if you need any help.
Curtis