I can't help you with transparency, but 'covering up most of the game screen' suggests that you're using the config menu instead of the on screen display.
If you haven't changed the mapping, ` (backtick, usually next to the 1 key) will toggle the on screen display. That allows you to adjust one slider setting at a time.
I don't know the reasoning behind this, but the on screen display is context sensitive. If you bring it up in-game, you can adjust the volume and most of the HLSL settings. However, if you toggle it while you're in the Slider Controls menu (where it's already visible anyway) you can adjust all of the sliders that appear in that menu without the menu itself being in the way.
The Slider Controls menu doesn't expose all of the HLSL settings, but it's a start.
--Nexusmtz