MTR 3.17 Supplementary Decks

Some mechanics, such as attractions, make use of an additional deck of nontraditional Magic cards.

Attractions are typically the only tournament legal cards that require an additional deck. Contraptions and planar cards use these rules as well if there is a tournament that makes use of them.

Cards in a secondary deck are not part of the deck or sideboard and do not count against any minimum or maximum deck or sideboard size.

Secondary decks have their own rules with respect to deck size, and this number can change based on event format, so be sure to check the comprehensive rules to ensure you are using the correct number.

They are presented and shuffled alongside the deck during pregame procedures, but do not need to be shuffled again if the player takes a mulligan.
Different supplementary decks must be kept distinct at all times during the game. Opponents may count the number of cards in a supplementary deck at any time.

You shuffle and present your supplementary decks like you do a normal deck. As there is no drawing from them, they do not take part in the mulligan procedure.

A player playing a supplementary deck must register the cards if decklists are being used and the contents of that deck cannot change during the event. In an event using continuous construction, players may change the contents of their supplementary decks between matches.

Basically supplementary decks follow the same common sense rules for regular decks.