Our topology consists of multiple branch offices. Sometimes our remote offices need to access file servers located in other branches.
From what I have read, the WAEs know about each WAE in the network path. If I have an intermediate WAE, how is the traffic processed for each remote end? Is it pass through on the intermediate WAE? Or should I deny that traffic through a redirect list on the intermediate WAE?
You are correct. If there is an intermediate WAE between both ends, that WAE will be aware that there are two end WAE's already performing optimization (through the Auto-Discovery process and the use of TCP options) and will pass-through any traffic for those sessions.
Please take a look here: