Z-indexes are such trifles that you may not realize their true value at once. However, using Z-Indexes is tricky. If you don't organize them right from the start, it may turn into a huge pain in the future.
There are different approaches to handling z-indexes of various elements. This article describes a neat way to managing z-indexes through keeping them as variables in a separate file: anadea.info/blog/a-guide-to-z-index