If you participate in the Amazon Seller Fulfilled Prime scheme, you will want to ensure Prime orders are dealt with quickly, and may want to set up prime-specific rules.
All Prime orders will be downloaded from Amazon with the word 'Prime' pre-pended to the selected Amazon shipping method, e.g. Prime Std UK Dom_2. If you wanted to set a Shiptheory shipping rule to target all prime orders, you can enter a custom shipping rule using a wildcard character to match anything after the word 'Prime', e.g. Prime*
If you wanted to target just UK, Prime orders, then add a "where country matches 'GB'" rule on top of the above, and so on.