Keeping your Photoshop files organized is always important as it will help you and others find layers quickly. Often the best thing to do is build this organization into your workflow so that when you're done, there is no need for clean up. One way to speed this organization up is by using folders. There are a few steps involved, but in reality this trick should only take a second to implement. Below is my file and a small batch of layers. When I create these watercolor backgrounds I tend to duplicate layers quickly so it's important to keep everything organized.
1. First, select the layers that you want to group into a folder.
2. Hit "cmd + g" and Photoshop will throw the selected layers into a folder.
3. Name your folders. Repeat until all the layers are organized.
4. If you want to take it one step farther, control-click the folder and set a label color.
There you have it. A nicely organized Photoshop file. If you can remember the shortcut "cmd + g" then use it while you're working and your Photoshop files will always stay organized.