You need to put the queue on server B (the Biztalk Server) For guaranteed delivery you need to use a transactional queue. Biztalk only supports local transactional queues.
Server A will have the MSMQ software and operate as an independent client i.e. it will store and forward messages if the Biztalk server is down.
You cannot use load balancing with MSMQ ( the queue can only exist on one server at a time). For fail-over you will need to cluster the Biztalk servers.
http://msdn.microsoft.com/en-us/library/dd897482(BTS.10).aspx
Disaster recovery is added complexity – the assumption is the entire data centre is lost and you must move every server to a new location. There are many variables that need to be taken into consideration here – network topology, web server switching, DNS, logging shipping databases or geo-clustering, recovery procedures, etc,etc. Do you already have a disaster recovery strategy/plan?