for about a year I've only been eating 1-2 times a day, all fast food in small amounts, 1 - $.99 burger, 1 - $.99 small fries, and that would be a meal. Lots of drinking alcohol contributed to my loss of apetite. Last week I changed my diet found a healthy food plan off this website (It's a 2000 calorie diet program) and have started that and an exercise routine, mostly for cardio so I can lose my beer belly.

Is it ok that I made these drastic changes right away? Last week I started jogging/walking during my lunch break- about 6-8 miles a week (2 miles a day). If I have the energy and time I'll walk/jog for another 20 min. at my treadmill at home. I'm probably going to start burning muscle, correct? So, I'm starting to try and find out what all protein foods I need to keep my muscle and burn fat, right now I'm eating tuna about every other day.

I keep getting this feeling/thought that's telling me that I should I start filling up on fatty foods (just increase my calories to a crazy amount so I have something to burn) for a few weeks atleast before have starting this diet/exercise program I've started so my body doesn't go into some kind of shock after a year of no nutritional food or even fatty foods, basically nothing but alcohol and all of a sudden change everything around. Am I wrong? I would like to be wrong and continue with this diet/exercise program, but I don't want to end up doing worst damage to myself from this sudden shock.

People tend to underestimate the body's "toughness". You will be fine, given you are not going out and exhausting yourself to early when you are unready and falling over from a heart attack.

Just like your body replenishes glycogen stores following exercise, it will also replenish amino acids as well. While there is some evidence that suggests that sustained (Way to much) endurance training can negatively affect one's muscle mass, the average exerciser is not going to notice any difference--especially if He/She follows a balanced diet of healthy foods. The only way you would notice muscle loss from Endurance training is if you are doing one of the following.
You are not eating enough protein
Your carbd WAY are too low.
You are not eating enough calories to support muscle growth.
You are not weight training.

EDIT
I forgot to mention though, If say you are 325 pounds (Hypothetically speaking) and you get up from a chair you are basically doing a 325 leg press, however lets say you loose that weight and drop down to 200 pounds. Your body sees it no longer needs the muscle mass to support 325 pounds so it will begin to "burn" the unneeded muscle. In order to prevent this from happen one must "trick" the body into believing it still needs this muscle. And this is done through weight lifting.

Make sure you're performing moderate to heavy resistence training (weight lifting) during your fat loss diet.

Failure to do that means your body won't be stimulated into keeping lean muscle. Having lots of muscle is NOT advantageous from an evolutionary standpoint...so the body will burn muscle if it thinks you're starving (due to diet changes).

Making changes isn't bad, but it will take your body a little while to adapt to the new lifestyle. Its no surprise you feel more energetic since the diet change. But rather than more cardio, I'd throw around a little iron. Weight training doesn't really burn fat, but adding muscle increases the number of calories you need to maintain your weight, which makes cutting fat a little easier.

How am I going to lose my beer belly if I don't work on cardio? I lift weights 3 times a week.

Supplement each other with the other (translation) Do both.