It is best you write to them and ask. People are quite prompt in replying. When you do, make sure that you explain the context of your experiments so that they can give you the best possible advice. I don't think we are allowed to post costs that are confidential on an open forum. I will inbox you with the costs on Geochips from our quote.
Remember that you can cut the costs down by reducing replicates and doing qPCR for statistical purposes on specific function or taxa.
Also, if you need help getting started contact [email protected]. Second Genome sells PhyloChips and also offers a simple service where you send in samples and receive back a full report.