TicTacToe.java

public class TicTacToe extends JFrame {
    private boolean initialized; // Default = false
    private XOButtons buttons;

    private int scorePlayer1;
    private int scorePlayer2;

    // Reset the board
    // Reset the markers, etc.
    public void resetGame() {
        this.scorePlayer1 = 0;
        this.scorePlayer2 = 0;
        this.buttons.resetMarkers();
    }

    // Set up frame, buttons, score, etc.
    public void newGame(){

        // If the application has not been initialized for the first time,
        // setup the frame with everything else
        if (!initialized){
            buttons = new XOButtons();
            // Set up frame
        } 
        // Otherwise, reset the game
        else {
            buttons.resetMarkers();
            // Do other stuff...
        }
    }

    // Play the game
    public void play(){
        // For each round,
        // a player chooses where to put their "X" or "O"
        // add scores, etc.

        // Then at the end of each round
        if (this.buttons.winCheck())
            this.resetGame();
    }
}

XOButtons.java

public class XOButtons {
    List<JButton> buttons;

    public XOButtons(){
        this.buttons = new ArrayList<JButton>();
        for (int i = 0; i < 9; i++){
            this.buttons.add(new JButton());
            // Do what you want with the buttons
        }
    }

    // Check to see if there is a winner
    // If so, announce the winner and return true
    // Otherwise, return false.
    public boolean winCheck() {}

    public void resetMarkers(){
        for (JButton button : buttons) {
            button.setText("");
        }
    }

    // Getters and setters
    public String getMarker(){
        return this.marker;
    }

    public void setMarker(String marker, int row, int column){
        int location;
        try {
            location = (column * 3) == 0 ? 0 : column * 3 - 1;  // Adding extra logic here to disallow negative values.
            location += row;
            this.buttons.get(location).setText(marker);
        } catch (NumberFormatException | NullPointerException e) {
            e.printStackTrace();
        }
    }
}