Hey everyone,
I built a Prusa Mendel with a RAMPS kit from Ultimachine that I soldered together myself. For endstops, I'm using optoswitches.
So let me start off by saying that I am a complete noob at software/advanced electronics... I am very confused about how to interface the printer with my computer. So far I have downloaded Arduino Alpha, Meshlab, OpenSCAD, and the Reprap console. I understand that the Arduino Alpha program is used to upload the firmware to my arduino, but that's pretty much the extent of my knowledge. I'm not sure how exactly to get the firmware on, what firmware to use, and what to do after that.

You are right, use Arduino for uploading the firmware to your Mega board.

Then use one of the many softwares available to control the printer from your PC. First stop is to calibrate it. Repsnapper or Pronterface are the two I've used. They have buttons for you to send manual motion commands to your printer, so you can check how long does it travel when you order 1, 10 or 100 mm. Once you have that, you need to make sure your firmware configuration is working ok (that + and - motion goes in the right direction) and that the endstops are working.

If all goes well, you can start printing calibration parts.

misan

Arduino needs to be set up to communicate with your Arduino MEGA board. Do this by selecting the model of Arduino board that you have.

You will also need to select the active com port of that board, as it appears in the device manager (assuming Windows OS).

Once the Arduino development environment is configured to communicate with your board, you can open up your firmware of choice (Sprinter is a good place to start).

The important file in the firmware is the Configure.h file. There is where you need to input things like whether or not you are using a heated build platform, the type of thermistors you have on the hot end (and build platform), whether or not you are using hardware/software endstops, etc.

Once you have everything the way you think it should be, you can upload the firmware to the board. If all goes well, the Arduino application will indicate that the upload is complete. Otherwise, you will see error messages. If you do get an error, it is most likely due to selecting the wrong board, or com port in the Arduino IDE configuration, and NOT the board itself.