I get you.... There are two meanings to the word time, one being the literal "time", as in 2 o'clock, the other meaning time as "in a different time".... So, no, 1 o'clock today isn't a different reality from 2 o'clock on the same day. I'm not that talented in conveying ideas or thoughts very coherently, unfortunately.
The problem is, the same with a film like Mulholland Drive, you can think you completely grasped the plot, or the director's intentions, but turning that thinking into words is the hard part.
I do believe there are two realities: The first one is the one we get to see during the major part of the movie, where he meets his girlfriend, floods the school, etc. The second one appears after Donnie travels through the wormhole, and ends up in bed, before the engine will wreck his room. Frank saves his life by getting Donnie out of his house in the first reality, thus creating a second reality where Donnie does live, the makers refer to this as a "tangent universe". It's really not that difficult, me trying to explain is
And this makes the movie sound like an intricate sf-movie, while it really is a beautiful story about a teenage boy that finds the world around him hard to understand.