You need to right click the task bar, go to Properties, then to the Task bar
tab and ensure  "auto-hide the task bar" option is checked.  (it's unlcear
from your question if you have actually done this....).

Anyway, the way to do it is the same in Vista as in XP as aforementioned.

I expect that when any actvity associated with the task bar (including those
popup alerts, which of course appear in the system tray (part of the task
bar) it will pop up to show the alert.

You can probably supress those alert notices within the application that
issues them (such as "new mail" messages issued by your mail client or
messenger or whatever)