You can change the dimensions of the thumbnail images (for example to landscape or portrait-style rather than square) by clicking the 'Change...' button in the 'Image Size' control panel on the 'Images' tab of JuiceboxBuilder-Pro. However, if your source images do not have the same aspect ratio as the thumbnail dimensions you specify, then the images will be cropped. The cropping will be centered and this cannot be changed within JuiceboxBuilder-Pro.
If I were to crop them by hand and replace those generated by the program in the folder, would that work?
Yes. You could replace the thumbnails generated by JuiceboxBuilder-Pro (in the 'thumbs' folder) with your own images. Just make sure they have the same filenames, otherwise you will need to modify the references in your gallery's 'config.xml' file.