Certain cards instruct you to place tokens onto the Battlefield (e.g. Silverfur Partisan, Aspiring Aeronaut). You may use token cards as those tokens, though you need not use those. Any physical object will do as long as you can clearly represent whether the token is tapped or not.
100.2. To play, each player needs his or her own deck of traditional Magic cards, small items to represent any tokens and counters, and some way to clearly track life totals.
Keep in mind that token cards are not considered cards as far as the rules are considered.
108.2. When a rule or text on a card refers to a “card,” it means only a Magic card. Most Magic games use only traditional Magic cards, which measure approximately 2.5 inches (6.3 cm) by 3.5 inches (8.8 cm). Certain formats also use nontraditional Magic cards, oversized cards that may have different backs. Tokens aren’t considered cards—even a card that represents a token isn’t considered a card for rules purposes.
This means your deck can't contain tokens.
Double-faced cards don't have the normal back other Magic cards have. Such cards would be identifiable in your deck, in your hand, etc.
One solution is to place your deck in truly opaque sleeves.
The other is to use a checklist card as a proxy when the double-faced card isn't on the battlefield.