Are you talking about WebHelp output? If so, as far as I can tell the height of the toolbar is determined by the height of the button images in the skin. I don't know a way to get both things you are asking for. To make buttons look like they are at the bottom of the toolbar, create images where the buttons sit at the bottom and the rest is filled with the same color as the toolbar. However, the button images are justified to the top of the toolbar, so they will cover up any logo you have at the top left. If you create a toolbar image with the logo to the right after the buttons, it won't be covered up by the buttons.
Hope this helps,
I believe I've documented this process in my Skinny on Skins file. You may download it by visiting the link below.
Also note that the download page has a link on it to use if you have problems viewing the file after you download it.