I'm about to start a project using the FAST Search Server and would like to know something about how we can scale the Search Server.
Can we setup multiple search server application pools or how does this work?
With FAST Search you are going to have a separate set of servers dedicated to document processing, indexing and other components. The configuration options are very flexible so you'll need to come up with the proper architecture based on your specific requirements for content freshness, query throughput, index size and redundancy. Your SharePoint application servers will only be responsible for crawling SharePoint sites. The topic is too broad for a short answer like this but there's plenty of information available on TechNet. Here's a good starting point: Plan search topology (FAST Search Server 2010 for SharePoint)