In your Tremulous console (to open it press the ~ key above TAB) type "/set cl_allowdownload 1" without the quotation marks.
This will automatically download the maps when the server loads them and you don't have them.
I've noticed that using autodownload puts the maps in C:\Documents and Settings\[User]\Local Settings\Application Data\Tremulous\Base, and that's a fragmentation issue as well as a searching issue (Local Settings is by default a hidden folder, as well as the Application Data folder within it.)
Is there any way to download straight to the main install path of Tremulous? Cut/paste of the downloaded .pk3s isn't to terribly difficult, but it would save a little time and performance speed if all the maps stayed in the main installation area, not on the other side of my hard drive.