data process and output is both on amazon ( input is free but storage and transfer costs $)
apologies if the second question was not framed properly, but it seems there is a fee to share output datasets between nodes on same master instance ?
Data transfer into Amazon's cloud is completely free. Data out is what costs money. See
http://aws.amazon.com/pricing_effective_july_2011/
What you're trying to do here would be loading data *into* amazon from our main server at
usegalaxy.org. I'm not sure what you're asking with the second question there -- in a cloud instance the master and worker nodes are all inside the cloud, and communication between them is both free, and very fast.
-Dannon