void Input(int Guess[][6], int Lines)
{
    //modify Guess as you please and the values in Guess from main() will change as well
}
//...

int Guess[Lines][6]; //as cire said, not valid C++ but I'm sure your teacher won't mind. Just don't get in the habit of doing it this way, alright :) ?

Input(Guess, Lines);

//...rest of code... 

    const int lines = 6 ;
    lines = 7 ;  // won't compile.  lines is constant. 

int main()
{
    int array_size = 6 ;
    int array[array_size] ;
}

 int main()
{
    int array_size = 6 ;
    int array[array_size] ;

    array_size = 10 ;
}

void Generate(int Ball[])
{
    cout << "Lets get those balls rolling...\n\n";

    for(int n=0;n<6;n++)
    {
        do
        {
            srand ( time(NULL) );
            Ball[n] = rand() % 49 + 1;
        }
        while(Ball[n] < BetLow || Ball[n] > BetHigh);

        cout << Ball[n] << "\t";
    }

}

            do
            {
                string input = "0";

                cout << n + 1 << ")\t";
                //Guess[Line][n] = 0;


                getline(cin, input); //cin goes to input string first
                stringstream myStream(input); //puts input string into myStream of type stringstream

                if (myStream >> Guess[Line][n]) //if stringstream detects that myStream can go into the array as an int type variable...
                {                               //loop continues as normal
                    if (Guess[Line][n] < BetLow)    //can't bet below 1
                    {
                        cout <<"Too low, try again! (1-49)\n";
                    }

                    else if (Guess[Line][n] > BetHigh)  //can't bet over 49
                    {
                        cout << "Too high, try again! (1-49)\n";
                    }

                }

                else //else stringstream CAN'T put myStream into the array...
                {
                    cout << "\nInvalid number, please try again" << endl << endl;
                }
            }
            while(Guess[Line][n] < BetLow || Guess[Line][n] > BetHigh);

int Compare(int Lines, int Guess[][6], int Ball[], int BonusBall, int Matches[])
{
    for(int Line = 0; Line < Lines; Line++)
    {
        Matches[Line] = 0; //resets counter per line to avoid winning on a line that you won on last round

        for(int n = 0; n < 6; n++)
        {
            if(Guess[Line][n] == BonusBall) //DOES NOT WORK
            {
                Matches[Line] = Matches[Line] + 1;
                cout << "BONUS GET on line " << Line;
            }

            for(int b = 0; b < 6; b++)
            {
                if(Guess[Line][n] == Ball[b])
                {
                    Matches[Line] = Matches[Line] + 10;
                }
            }
        }


        if(Matches[Line] > 0)
        {
            cout << "\nYou scored " << Matches[Line] << " on line " << Line + 1 << " of " << Lines << "!";
        }
    }
}

    //---BUBBLE SORT CODE-------------------------------------
    for(int Line = 0; Line < Lines; Line++)
    {
        int flag = 1;

        for(int n = 0; n < 6 && flag; n++)
        {
            flag = 0;//resets flag

            for (int bs = 0; bs < (n - 1); bs++)
            {
                if(Guess[Line][n+1] < Guess[Line][n])     //if the next in the array is less than this one
                {
                    int temp;
                    temp = Guess[Line][n];             //swap elements using temp data storage
                    Guess[Line][n] = Guess[Line][n+1];
                    Guess[Line][n+1] = temp;
                    flag = 1;               //indicates that a swap occurred.
                }
            }
        }
    }

void Generate(int *Ball, int &BonusBall)
{
    cout << "Lets get those balls rolling...\n\n";
    srand ( time(NULL) );

    for(int n = 0; n < 6; n++)
    {
        do
        {
            Ball[n] = rand() % BetHigh + BetLow;
        }
        while(Ball[n] < BetLow || Ball[n] > BetHigh);

        cout << Ball[n] << "\t";
    }

    BonusBall = rand() % BetHigh + BetLow;

    cout << "And the bonus is..... " << BonusBall << endl << endl;

}