I am doing this assignment in my Java class. I have never done any programming in my past so I am a complete beginner. I have typed up a program that will ask for employee name, the hourly rate, and the number of hours worked. The program needs to run in a loop unless "stop" is typed as the employee name. There are no errors in my code and it builds/runs OKAY except for the fact that it doesn't stop running when stop is typed into employee name. I have reviewed my code and did some research online but I cannot figure out what I am doing wrong here.

package payrollprogrampart2;

import java.util.Scanner;

public class PayrollProgramPart2 {    //declares class

    public static void main(String[] args) 
        Scanner input = new Scanner(System.in);

        String cleanInputBuffer;
        String employeeName;
        double hourlyRate = -1d;
        double hoursWorked = -1d;
        double weeklyPay;
        boolean end = false; //is the input name stop?
        while( end == false ) //as long as end is false, continue

            System.out.print("Enter employee name or enter stop to quit: ");
            employeeName = input.nextLine();
            if( employeeName.toLowerCase().equals("stop"))
                end = true;

                    while(hourlyRate < 0)
                        System.out.print("Enter a positive hourly rate: $");
                        hourlyRate = input.nextDouble();
                    while(hoursWorked < 0)
                        System.out.print( "Enter a positive number of hours worked: ");
                        hoursWorked = input.nextDouble();
                    weeklyPay = hourlyRate * hoursWorked;

                    System.out.printf( "The employee %s was paid $ %.2f this week", employeeName, weeklyPay);

                    cleanInputBuffer = input.nextLine();

Here is the output:

Enter employee name or enter stop to quit: Kayla
Enter a positive hourly rate: $11
Enter a positive number of hours worked: 80
The employee Kayla was paid $ 880.00 this weekEnter employee name or enter stop to quit: stop
The employee stop was paid $ 880.00 this weekstop
BUILD SUCCESSFUL (total time: 15 seconds)

How can I get the program to skip to a next line when asking for second employee name? Also, when I type stop into employee name, it doesn't stop the program and it gives me the amount from the previous employee but names the employee stop. Why is this? I am so confused!! :[

You can skip to a new line any time by using a \n (newline) character. eg
will print a newline followed by Hello

Your loop's end == false test is only executed at the start of each iteration. So in your second iteration you enter stop, set the boolean, but you still execute the rest of that iteration before looping back to line 17 to test the boolean end exit the loop.
One solution is to use a break; statement to exit the loop immediately, eg (pseudocode)

while (true) {
   get the name
   if (name is "stop") break; // exit loop immediately
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