If you want to add mods or themes to your stock rom you will need to first Deodex it. Most mods and themes simply wont work when the rom is odexed. However Odexed Roms tend to perform a bit better under certain unique circumstances. There are plenty of modders who have deep seeded beliefs on which is better. If you ever wanted to theme you would have to master the skill of deodexing and odexing a Rom. Both can be incredibly time consuming. Developer "M_J_Nazari" has developed a toolkit to fix this problem.
The tool is pretty much straightforward in its use. If you can follow directions you will have no problems. This tool is mainly for those who are interested in themeing or creating custom mods. If you develop a theme that works for deodexed roms this tool will make it easy for you to test the work on odexed roms as well.