This single box will hold all your qualifiers for several months. At some point, you will begin to outgrow your box. Then it will be time to expand. Here's how.
Get several more cardboard boxes. Find an out-of-the-way place to store them, in the basement, under the bed, or in the garage. If you're lucky to have an extra bedroom with a closet, you can turn a corner of it into a refund room.
Examine your original box and decide which categories are overflowing. Maybe your "Baking/Cereal" file is loaded to capacity. Take one of your new boxes, put a few file folders and Ziploc bags in it, and label the entire box "Baking/Cereal". Take all your proofs of purchase from this category and break them down into smaller groups. Your groups will include:
Kelloggs cereals
General Mills cereals
Quaker cereals
Post cereals
Ralston Purina cereals
Pillsbury
Duncan Hines
Betty Crocker
If the proofs of purchase are small (like the UPCs from cereal boxes), use Ziploc bags, one for each division. You'll have a Ziploc bag for Kelloggs cereals, one for General Mills, one for Post, etc. If the proofs of purchase are large, like a flattened muffin box, use file folders labeled with the appropriate category: "Pillsbury".
This second box is the final resting place for your qualifiers until they are needed for a refund.
There are refunders who have come up with truly magnificent filing systems, with many, many different boxes. But that isn't required, especially when you first start out.