This my new design for a 3D printed command tray that was design to hold all of your ship components with a minimal footprint. I have printed several prototypes and they work very well. It has space for all of your tokens and up to 15 damage/upgrade cards. As well as counter for your total damage. Links below.
Shapeways:
https://www.shapeways.com/product/TXANPC342/full-armada-ship...
Thingiverse: