ichal_spy's method may cause a vBulletin upgrade to overwrite the custom logo.
I prefer to upload my own logos under names like bb_logo_theme.png, where bb is the board name and theme is the name of the theme.
Then, edit the particular theme(s) in Style Manager (see ichal_spy's post above for path), replacing "vbulletin3_logo_white.gif" with the path and name of my new logo.
vBulletin's upgrade scripts don't change settings in this area.