Yes: you can use the New Game with Options... item under the Game menu to choose how many decks you wish to play with.

You don't need to do it every time you start a new game, since it will remember the last used setting.

The same menu item can be used to set the options for other games as well (for instance, in Klondike you can use it to change the number of cards dealt when clicking on the deck or to allow partial column moves).