Option "twosided" in b2cs menu works exactly like this: during export it automagically duplicates faces and flips normals while retaining uv map.
However, it causes (or was causing) problems with lighting in CS, opposite faces cast shadows on each other, although they should not do it. So - better and more predictable effects can be achieved by duplicating faces manually and pushing them away from each other a little bit.
I'm not sure, what is Your problem with transparency. Options in b2cs gui don't affect the way a model is displayed in Blender. For this to work you need to go to "uv face select" mode and push button "alpha" on "texture face" tab, do it for each face wich has texture with transparency information.
Still, in Blender's 3D workspace transparency glitches always appear (at least for me). Renders should look OK though. Also try to play with button "ZTransp" in material settings.
Setting priority and zmode for items will not help at all, because those settings in CS affect
objects, and you are supposed to produce
factories (libraries), which then will be used to create objects placed in the world by game engine, and this is the game engine, which will decide what will be priority, mixmode, zmode etc... However, by preparing
material in proper way you can get good results - find in b2cs gui (material menu, section: texture) option "binary" and set it to true (I think it was called texture_binary in older versions of b2cs). This usually gives best results with transparency in CS (although it does not help with translucent textures).
BTW: question for Karyuu: will those object be of type sprite3d or genmesh ? Or maybe something else is planned ?
One more comment about transparency in CS - it often works unreliable and unpredictably and it is hard (or even impossible) to make an separate object which would always look good in CS

. So don't worry too much, I hope that the new CS renderer will deal better with that.
Edit:Note about using "twoside" option: remeber, that model after export will have 2x more triangles than shown in Blender.