Need help in mounting fixed cut glass windows

We are building a cedar home and will be using cut glass(double panes with a dark spacer) windows mounted in cedar in several areas. These windows will not have any kind of trim, will be cut to fit our specific openigs, will be stationary and won't open. They will be mounted between some kind of cedar trim pieces and sealed with some kind of silicone seal. I would like suggestions for the best way to do this to minimize the possibility of having water leak by the seals and into the framed opening that is attached to the structural wall.
Any suggestions for the best method or references to web sites that might explain this will be appreciated. I am sure this is common in cedar and log type homes. Thanks for any help.
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