Are they currently one material? Have you tried defining the two rock parts, and the glass type material as two different materials within a multi-material? So one material will applied to the rock using normal parameters, while the other material will be applied to the glass type material and us the alpha settings.
This took me ages to work out too! in the material editor, by the opacity setting there is an opacity value you can switch between Alpha Blend and Alpha Test. alpha blend produces soft and semi transparent results, you pretty much jack the slider up until you get something you like. (…
yes, in general (in most engines for that matter) its better to split transparent and alpha based materials from each other to help with sorting and lighting. also make sure that you save the texture with the transparency alpha channel as a cryTif, not a normal Tif to make sure that the Alpha information is correctly…