These are very general questions. Can you perhaps post specific, individual questions that members of the CODAP community can respond to?
One thing to know is that CODAP is “static.” I.e. everything takes place in the client’s browser. Interaction with servers is entirely optional. Typical server interactions are for save and restore of CODAP “documents” and logging user actions. But the client need not set up these interactions. So you should be able to integrate CODAP with hosted applications quite easily.