1. If i created a new install packages using SEPM at site B and install on a client pc, will the PC reflect on both sites SEPM?
It will reflect ob both sides of the SEPM.But it will point ot only one sepm for policy and definitions
2. can i configure site B all clients to download liveupdate definitions from another server instead of site A server? Is it using policy?
You have that option in Replication settings.The Content(Definitions) will also be replicated between these sites if you configure it.
3. if i made any changes on sites B,will all the changes sync to Site A?
Yes.Thats how replication works.You can schedule and what time you want both sites to replicat,Bydefault it is the first SEPM that decides when to replicate.
Ports used for replication
8443 (By Default ,Unless you have changed it)