Check engine light blinks

Drove the car from MO to WA--no problems. Everythings great for 3 days & then out of no where "check engine light" & rough driving. Engine never cuts out just a little rough. I discover that son driving car has only been putting "regular" gas in car. Car low on gas, I take to station --fill w/ "premium". Also add 1 bottle of "engine cleaner". Drive car around. Use 1/4 tank of gas. Seems better, less rough, but engine light still come on.
Ogg not know what to think. Is possible that there be engine belt slipping? Is possible engine "gunked up by "cheap" gas? Car drive mostly good now. Why engine light not go off? Is Ogg possibly do engine damage by continuing to drive? Please advise. I just had the throttle body replaced in my 2000 beetle two weeks ago for $900+ . What a shocker! My car had been stalling out at red lights and slow turns, so it was a necessity. It took a little while to get over the financial drain. I was beginning to recover until...tonight. My car spontaneously began running roughly, as the check engine light came on, blinking at triple intervals. I'm so frustrated with this car! It's always something, and I don't know if patching it up is even worth it anymore. Why can't the new beetle be as reliable as their vintage "sisters"?