I have a set of four bell pepper plants that I am growing in 12" containers in my backyard. They've been growing alright until the fruits on the plants have started to develop what appears to be a rot on their skin. What could be causing this? I water them well every two days and they get 6-7+ hours of sunlight a day. This is my first time ever growing vegetables by the way.
Here are some pictures since this is probably impossible to diagnose without:
This is almost certainly blossom end rot (BER), a disorder that is usually caused by fluctuations in the plant's water supply, leading to a calcium deficiency. It affects a number of plants, including tomatoes, squash and eggplant. On peppers, the lesion is usually a tan color in the early stages, later turning brown or black, and can affect the side of the fruit, as in your first photo, as well as the blossom end.
You're right to water your plants thoroughly (superficial watering could cause them to surface-root, and become stressed), but once every two days may be over-frequent, unless, of course, the ambient temperature is very high, and the soil/compost is drying out very quickly; it should be slightly damp most of the time, not wet. Over-watering washes calcium out of the soil and is another cause of BER.
You will find detailed information/links about BER and steps you can take to control it, in my answer to a similar question here. There is also a good overview of the problem here
