How can I keep track of my sideboarded cards in a physical Magic deck?
Write down your sideboard in a list and keep that with your deck. You might want to keep note of it on something durable in your deck box, for instance.

When you want to reset your deck and sideboard to their default:


Take a look at your currently sideboarded cards, and the sideboard list you wrote. Set aside the ones that belong in your default sideboard - put these together.
Find the remainders in your deck, and put those together with the cards you set aside in step 1, until you have your entire sideboard set aside in a pile.
Everything remaining that is not in that pile must necessarily be a part of your deck, so shuffle it back in.


You'll now have your default sideboard and, by exclusion, your default deck.