1> Check the manual for "ent_setskin". Is that what you mean?
2> I believe so. Check the manual under "d3d_autotransparency". But this only applies to BMAPs and therefore panels. It wont help if the BMAPs you are speaking of are used as skins. (there is a chance it MIGHT work, but Ive never tried it...)
Best of luck.
"There is no fate but what WE make." - CEO Cyberdyne Systems Corp. A8.30.5 Commercial