If you have 2 boxes targeting the same page, the topmost lightbox in the Box List takes precedence.
Other factors may affect placement as well. For example, if you set a rule like “Display until Form Submit” on the topmost lightbox, after it submits then the lower-priority lightbox will always be displayed.
Typically, when two boxes are eligible to display, they will do so back-to-back. You can prevent this on the same pageview with a Master Rule. An exception is Inline Boxes, which can display at the same time as Lightboxes, Sidebars, and Banners. In addition, Inline Boxes configured to “Always Display” in the Widget Accordian will always display, regardless of Box conditions or priority placement.