I'm going to assume you're using Mac, since only Mac does this.
If you are using Mac, then here's what you do;
.pk3 files are basically .zip files that are renamed to a .pk3. In order to turn the unzipped maps into .pk3s, simply right-click (or ctrl-click) on the folder and select "Compress [folder name]". Once you have done this, rename the new .zip file to a .pk3 file. Once you have done this, place the .pk3 file into your "Tremulous/base" directory. That should work.