I take it you are familiar with the concept of shaders controlling the actions of textures that you wish have transparent areas.
If you do then this link http://www.heppler.com/shader/shader/section7.htm should help you.
If you are yet to understand shaders then its a different matter.
This one looks good too
http://www.qeradiant.com/manual/Q3AShader_Manual/ch06/pg6_1.htm
Hope these help you out, the key i think is to ensure that you save in 32 bit TGA mode so the alpha channel is saved, then you need to look at the shaders of one of the simple alpha textures.
This is the shader used for the carpets in Oasis.
textures/siwa_props_sd/siwa_carpet2
{
qer_editorimage textures/siwa_props_sd/siwa_carpet2.tga
cull disable
surfaceparm alphashadow
surfaceparm nonsolid
surfaceparm pointlight
surfaceparm trans
{
map textures/siwa_props_sd/siwa_carpet2.tga
blendfunc blend
rgbGen Vertex
}
}
Give it a try and come back if you need further assistance.
<DJ>