I read in a magazine recently where they had a Nova painted at Maaco or something and put a coat of clear over the one stage enamel, instead of using a base/clear system. I thought you werent supposed to do that, due to the clear having a "magnifying glass" effect on the paint underneath or something. Can anyone tell me the pros/cons of this and has anyone had this done long term to see the effects? Also, would i wet sand before shooting the clear?

 

Yes this was the way it was done before the true base clears were developed.
Actually most show jobs were single stage and wet-sanded between coats. (three on and one off) Then for a finishing touch, mostly with metallics, a couple coats of clear added for durability and gloss retention.
Depending on your color, you could still do this, yes you will have to wetsand the entire car, assuming the paint is more than a week old.
You may need a mist coat of the color over the old color. Metallics will require a couple coats of color to get the stripes out and the new metallic to lay down.
Depends on your time frame and budget, use a compatible clear.