I'm new to arduino so please excuse me for my questions. I'm starting a project where I want to use the board to control a stepper motor. I want the program to be able to take inputs (like pop up windows) where it can prompt the user to input how many steps the stepper motor should move and then load the program to the board. Is this possible with the arduino?
Very possible and something many have done. There are two project phases to consider.
Your Arduino program (called a sketch) is created using the Arduino IDE software. When properly programmed, your Arduino program would communicate commands and data with the PC using a simple serial comm port channel, one character or byte at a time.
Your PC program has to be written in some programming language that can utilize a standard serial comm port link, most do.
So you need to learn to use the Arduino IDE with it's version of C/C++ programming commands and you will have to have experiance or also learn some PC programming to accomplish your goal.
Well you found the right place for the Arduino stuff, here is the link to the reference site with lots of stuff to check out:
For the PC side I can't help much, I don't program much on the PC side and a lot depends on what you might already know. If you list what operating system you use, windows, apple, linux maybe someone here can make a recommendation for you.
One way to accomplish what you want is to write a Java program that runs on the PC. The PC connects to your Arduino board via a USB connection. The USB connection will look like a serial port (COM1, COM2, COM3, etc.) to the PC.
The Java program will prompt the user for input. It will package up the values the user entered and write them to the appropriate serial port.
Meanwhile, back at the Arduino, your Arduino program (aka sketch) is reading from the serial port. When it reads in the values sent by the PC, it uses those values to manipulate the stepper motor, or whatever.
There are lots of examples showing how to do things on the Arduino like read from the serial port and work stepper motors. You can find those examples on this site, along with the documentation for the library routines.
There aren't so many examples of the PC side program, but it's nothing special. It just has to be able to accept user input, format it, and transmit it out on a serial port.