Both options are possible. You can set up a script to perform a find for a specified store. Here's a thread on scripted finds. The examples should provide you with some ideas on how you might set up such a scripted find: Scripted Find Examples
You can sort your inventory transactions in a sort order that includes the store. In fact, by playing games with the specific sort order, you can get different formats to a summary report on your inventory transactions.
Sort where the store is specified first, then by product and you'll get a report divided into two parts, one for each store. Sort by product, then by store and you'll get a report where you see totals for each product with a subtotal break down for each store for each of those products.
This tutorial on summary reports may help you sort that out: Creating Filemaker Pro summary reports--Tutorial