Honestly the best answer I can give you is to find a collaborator to help you out. While we on a forum can certainly answer lots of technical questions and point you in the right direction, the best way to learn something like this when you don't have any idea where to start, is to collaborate with someone if at all possible.
You should also be reading extensively from the literature. Metagenomics analysis of environmental samples is a huge field. There are tons of seminal papers in this field and lots of different programs out there. I can personally recommend software and pipelines developed by the Langille Metagenomics Lab and the iSEEM project from Jonathan Eisen's lab