Place "transparency" folder in C:\ and rename "System Transparency.ex_" --> "System Transparency.exe"
Then, if you want to load transparency at early boot, just apply the set-at-boot.reg file and reboot.

To change settings, right click on the tool icon in the systray --> Setup and info.
For suggested settings see the screen in this folder. 

If your settings are not loaded after rebooting the system, go in your Documents and, if there's systemtransparency.ini, open it and change settings manually:
[Settings]
trans=235
rclick=1
tbar=1
smenu=1
tool=1
explorer=1
notes=0
desktop=0
wmp=0
thumbs=1
op=
firefox=0
chrome=0
ie=0
deskbutton=0
mouseclock=0
alttabber=

If you are getting strange behaviours on your desktop after applying transparency (e.g. delayed overlays), try this steps:
- close the transparency tool and delete the .ini file in your documents folder;
- apply the reg to unload it at boot;
- load the default Aero theme;
- reboot;
- load the Abisso theme; 
- open the transparency tool ("Setup and info") and set your values (like in my suggested settings screen, DISABLE transparency for browsers and for desktop and icons), then click OK;
- apply set-at-boot.reg;
- open the .ini file in your documents folder and change values accordingly to the ones set in the tool (without opening it another time).