So as I started this adventure into weight loss I decided that calorie counting would be a good way to start. I started by logging everything in a small notebook and I am realizing that my daily intake is EXTREMELY low...like under 1,000 calories a day
I know this isn't good, especially since I have started working out.
I just don't know what to do or what to eat.

Care to share your food log? That might help us help you! :0)

Cheese is an ok suggestion, but the healthy fats are a great one. Heathly fats = avocados, olive oil, nuts and if you're feeling adventurous and can keep it at about 100 cals, dark chocolate. Extra veggies is always a good idea, I know they are still low cal, but still a good place to add cals. Add some humus to raw veggies for some extra protien.

I was aiming for 1200 a day and getting to about 1000 and was told by the posters here AND my dietitian that that was waaaaayyyy too low for me. Have a bigger breakfast like oatmeal. How about adding in some snacks? Cottage cheese, fruit, yogurt, etc.