I am using Google chrome and it puts it on top taskbar when chrome is open but I want it on the bottom taskbar.
Which bottom bar are you referring too? If you are referring to the Windows Taskbar, then this is not possible. The extension lives beside the address bar.
If you are referring to the new Chrome Apps button, then we might consider adding this in future updates. Feel free to add this to our Votebox: http://todoist.com/Vote/