I don't think there's a right or wrong answer to this really. I have dozens of token bags since I, like the OP, bought all of DK's stuff and each of them come in a separate module or folder. I did get some from somewhere which I put into a single bag. The point of the above is not to share vast numbers of tokens with players (so keep all of your tokens in the host folder - not the shared one), and not to have lots of bags open when you play. So when you are creating NPCs or whatever you need to open the bags to find the tokens you want but afterwards you close them up. So basically whether you have then in one folder or 50 folders is a matter of personal preference.