If you are referring to a navigation menu (which is unrelated to your Juicebox galleries), then make sure that your menu does not use any global CSS rules that your Juicebox gallery has no option but to inherit.
If the problem that you are experiencing is that your menu is a drop-down menu but that it does not appear on top of your Juicebox gallery, then give your menu's HTML elements a large 'z-index' value so that the menu is always stacked on top of the gallery (and does not disappear behind it).
If you are currently using a menu and would like me to take a look to see if I can determine exactly what the problem is (and perhaps suggest a solution), then please post the URL to your web page so that I can take a look.
If you are looking to use a menu to switch between different Juicebox galleries on a web page, then please see the 'Switching between Multiple Galleries using JavaScript' example in the Embedding Multiple Galleries support section.