With Juicebox-Pro, you can set the thumbsPosition (TOP, BOTTOM, LEFT or RIGHT) and you can also specify the maxThumbColumns and maxThumbRows.
As an example, you could set thumbsPosition="LEFT", maxThumbColumns="2" and maxThumbRows="6" to have 2 columns of thumbnails to the left of the main image.
In such a configuration, there will always be 2 columns on thumbnails but the actual number of rows will depend on the space available in the user's browser window.

Here's a sample gallery with this configuration:

For reference, a complete list of Thumbnail Options can be found here.

You can force the gallery to be displayed in Small Screen Mode (where thumbnails and main images are displayed on separate pages) by setting screenMode="SMALL" (in JuiceboxBuilder-Pro's 'Customize -> General' section).

Please see here for details on Screen Modes.

In Small Screen Mode, a grid of thumbnails is displayed and when one is selected, the large image is displayed (replacing the thumbnail page). The user can return to the thumbnail page via the Thumbnail Button on the gallery's Button Bar.
Click here for an example.

Thumbnails can be sized using the thumbWidth and thumbHeight options (all thumbnails in a gallery share the same dimensions).
Thumbnails in Small Screen Mode are displayed on pages. If there is not enough room to display all the thumbnails on a single page, then additional thumbnail pages are created and the user can scroll through the thumbnail pages via the thumbnail navigation arrows (by setting showSmallThumbNav="TRUE" in JuiceboxBuilder-Pro's 'Customize -> Thumbnail' section).

Try resizing your browser window whilst viewing the sample gallery to see how the thumbnail page reacts to different viewport sizes.