Users non-logon to local DC and managing Replication

I manage a Windows 2003 R2 single Forest single domain, multiple sites with multiple DCs over a 64k WAN link from head office to branches in a hub and spoke topology. All brach DCs are GCs

1.Users are not authenticated by their local DCs even though various subnet are created and mapped to repective site.

2. I need to control authentication traffic. Will disabling KCC and manually creating replication partners and replication schedule resolve my issue?
Are there known issues with this apporach?
Any suggestion as to Users non logon to local Dc and managing replication will be highly appreciated