i made a today theme with a bottom dock. but now the navigation is all messed up. like i have to move the ball up in order to get to the icons on the bottom dock. how can i change it so that the bottom dock will be horizontal and the stuff on the top is vertical?

There should be a selection box at the bottom of either the first screen, or the second screen, in Theme Builder where you can select the type of navigation you want. I have found in the past this will reset itself so make sure you check it each time you edit the theme.

2nd button down on the theme creator i for the main screen. The bottom option is navigation. Click the middle icon and make it your first item then select the navigation and repeat that for all the icons you have on the bottom dock.