By default, Bunch reads plain text files from a folder at
~/Documents/Bunches (that’s a folder called “Bunches” in your Documents folder). You can add a new folder using the Add button next to the Bunch Folder in Preferences (possibly to a Dropbox or iCloud folder where you can sync with other machines). The dropdown menu there will let you switch between any Bunch folders you’ve added.
Tip (kinda): when you change the Bunch folder location, it doesn’t move or delete any of the Bunches at the previous location. That means that (in a fairly inelegant way) you can use different folders for different sets of Bunches. You can also quickly switch sets using the setPrefs URL handler from other apps.