How do I make the domain bake the fluid object? I'm following Blender Guru's guide for Introduction to Blender's Fluid Simulator and I have everything all set up, a cup with an object inside of it and a cube. The cup is set as an obstacle, the object inside the cup is set as fluid and the cube is of course set as the domain. The cube is surrounding both objects as well.

When I go to bake the domain cube the fluid that shows up is outside of the cup (As shown by the rectangle in the picture below) and nowhere close to the same shape of the object that I have set to fluid. The confusing part is, I did the exact same steps as the video tutorial and in the video it works but mine doesn't. So how do I get the fluid to be in the cup when I press bake? Not sure if I'm just an idiot, but any help as to how to get the fluid in the proper shape and spot would be great!
This is because of the fluid quality. 
Working with higher resolutions and some other settings that I will explain can help you enjoy a much smoother and more realistic fluid simulation with Blender's fluid simulator. 
Here are a few tricks:   

1) Use subdividing on the domain AFTER baking the simulation. This will smooth out your simulation and fake the look of a high quality simulation on quality 120. It will not entirely work without-  

2) Using surface smoothing. Adding a high level of surface smoothing actually improves your simulation by a ton when combined with a little bit of subdividing. Settings for this here:

Do not use the subdivision setting here or else baking will really be a time problem.

3) Setting fluid viscosity. Adjusting the viscosity of water just a very tiny bit will actually improve the simulation if you set it to be slightly more fluid-like.

4)Set the time on the fluid simulation accurately. Having correct timing and speed is a big factor in realistic fluid animations because without the correct time starting and stopping your simulation will be slower than real water. To correctly set this you must set the start time to zero, or if you want to start your simulation at frame 48 you must set it to 48/the framerate of your animation. Now set the end time to the length (in frames) divided by the framerate.

5) If you decide to make a very high quality fluid simulation (and have the hardware to do so), uncheck the remove air bubbles box. This will add a more real look to the simulation by adding small bubbles near the edges of the fluid, and where the inflow adds fluid. Here's a pic:

I hope these settings help you!