What happens is a user logs into Kayako using their details from the linked application. It does not work the other way around (ie if a user registers on Kayako, they will not have their details added to IPB's database). The best thing to do is disable registration on Kayako.
Currently it is not possible to have multiple loginshares on the same template group. You could setup multiple template groups and have a loginshare for each one. The manual explains more about template groups if you want to look into this option (
http://docs.kayako.net).