I just pushed out a new version of Searchify
that allows you to run multiple instances on the same page. Please check your stylesheets if you have customized versions. I've tried to keep it backward compatible, but basically you should be using class names instead of id's now.
You can see a store with 2 search boxes on it here: http://daisypark.myshopify.com/
(the store is currently under development and there are some z-index issues not related to Searchify).
As part of this change, their is a slight change in the way it works - it now shows what it is searching for as you type. This provides more immediate feedback for users. Let me know what you think.