Update - thanks everyone for the suggestions, and when I was messing around with it today, I had completely forgotten that I changed the tension dial on the machine which is why it screwed everything up. I didn't know that the reason the stitching is a mess on the bottom is due to the tension on the top. I learn something new whenever I come here. So, as of now, problem solved.
I also think I will get another extra bobbin case just for different thread. That is a good suggestion! Thanks!