This plugin will export the layers in your image as png files, using slightly modified functions from Chris Mohler's Export Layers as PNG plugin, then run Sprite Sheet Packer on them to generate a texture atlas and corresponding map (text file).
Important: Sprite Sheet Packer is needed for this, as well as my Miyagi skin exporter. I have attached it here, but you can also download these binaries from this link.
I wrote this to speed up the workflow of creating Miyagi Guis (see below). To cater for your particular system, you can write your own map exporter for SSPacker, then replace the binaries I provide below to include your exporter. Layer groups will be exported as single layers.
Sprite sheet packer is a really cool open-source project. My exporter is not absolutely necessary - if you change the plugin to export the map to a different format, it will run fine. My exporter saves the map as a Miyagi skin file - Miyagi is a popular Gui system for Mogre, an awesome open-source .NET graphics engine (Managed Ogre). See this thread for more details on my exporter.