What do I do with fuel, distance, and time to descend and climb, on nav log?
Realize that both the climb and descent are taken from the en-route section.

I always calculate climb first and determine where I will reach top of climb on the sectional chart. I then calculate descent and figure out when I need to descend on the sectional chart. The distance in between is my en-route section.

From reading your question, it seems you calculated en-route from departure airport to destination airport. You don't want to do that.