A Juicebox gallery is embedded into a regular HTML <div> container (see the Embedding Guide for details) at dimensions specified by the galleryWidth and galleryHeight configuration options in the embedding code. If the gallery <div> is the only container on the web page and the gallery has a width of 100% and a height of 100%, then the gallery will fill the page.
However, the gallery does not need to be the only <div> on the web page (and the gallery's dimensions do not need to be '100%', you can use other percentage values or fixed pixel values such as '600px').
Take a look at the Side Menu and Top Menu sample pages in the Resizable Gallery support section for examples of galleries with other <div> containers on the page. These examples are full page demos (where everything is visible without the need for scroll bars) but Juicebox galleries can be embedded in regular scrolling pages, too (see here for an example). It just depends on the layout of your web page and where you position your gallery <div> (and the dimensions of the gallery) as to how the gallery will look on your page.
You can view the source of the demos in your browser and copy/modify them to suit your own needs if you like.
I hope this helps to clarify things.