Seems like there are two different situations here. If the user can add more than one of a specific item to the bundle, Option A will not work, since it is a toggle - add it or don't. Option B appears to allow the user to change the NUMBER of a given item they want to add. I think your solution needs to take that requirement into account.
I can't tell if the box at the top is meant to just be a filter for the list, or an area to reflect what products the user has selected FROM the list. If it is a filter field I'm not sure how those capsules got in there or why it is not simply a text entry that immediately filters the list below. Either way I think it would be a good idea to have an area of the screen that DOES reflect all of the items the user has selected or deselected so they can see their updated bundle at a glance before they commit to it.
UPDATE: Based on our exchange below, here's a quick mock-up of what I envisioned, including both a way to remove items from the capsules as well as show how many of an item is represented by each capsule), and keep the Add New function below that, with the filter box:
Just a thought, take it for what it is.