Hi Andy
You may want to check out our Shopify Assistant app (http://www.shopifyassistant.com/).
It is designed to run tasks in the background to synch inventory based on orders placed.
ie. If you received an order for Design A on a small red and Design B on a small red, then you could set a task to deduct 2 x small red from your master inventory of that product.
There is a 7 day free trial so feel free to test it out. If you need any help, please create a support ticket at
http://support.shopifyconcierge.com/home
Thanks
Shopify Concierge