In the flashback scene for Season 2, Episode 6 "Anniversary", the viewer sees what transpired during the time when Frank and Marie were separated.
With actor Ray Romano playing a younger Frank, and actress Patricia Heaton playing a younger Marie, the two characters get into an argument because Frank wanted to salt his food. Frank eventually leaves while Young Ray and Young Robert are watching "Wild Wild West" and "Bonanza" on TV.
In order to get his parents back together, Robert tampers with Ray's bike, so that it collapses and Ray goes flying over the handlebars and brakes his arm. Frank then stops by often to check on him, and everything began to work out again. Frank and Marie get back together. And Are Probaly divorced in 2006