First themes work either with Customize or Summerboard. In Installer there are two categories of themes, one for each app.
I use Summerboard, and when you install a theme it goes to:
/var/root/Library/SummerBoard/Themes/ (if you are in 1.1.2 and lower) or
/var/mobile/Library/SummerBoard/Themes/ (if you are in 1.1.3 and higher).
Then to choose a theme you must lauch Summerboard and select it !
Like i said you select the theme from Summerboard itself (the app name on your screen should be SMBPrefs). Then go to "Themes" and pick one you installed via Installer!