To create SLA & setup Escalation to supervisors, Goto Setup > SLA Settings > Service Level Agreement and follow the steps. For more, refer SLA and Escalations.
Yes, support agents can be associated to multiple Departments. Goto Setup >Admin Settings >Users >edit the Support Rep and associate departments to the Support rep.
No, it is not possible to restrict a particular Departments for selected Customer Portal users. Once a Department is made "Public", all Customer Portal users can access that particular Department.
Yes, you can split a customer's reply as a new request. Say, you respond to a customer's request and resolved his issue1. He then thanks you and emails you about another issue2. In this case, you can split this issue2 as a new request and assign it ...