Trying to setup an automatic alternating function to alternate outputs

The first digital output is setup to switch on at a certain value, lets call it 60% and to switch off at 20%.

Are you talking values or percentages? Where is the value coming from? No one is going to steal your idea. Quit with handwaving, and tell us what you are talking about.

      if ( Measured_Value >= Relay2_On_Val )        // Trigger Relay 2 on as well if the value is still rising. This indicates that the first pump is not able to pull the level down i.e.

There is no excuse for such a long comment. You aren't writing a novel. You ARE allowed to use more than one line.