Heating problem

I have been looking at my heating system in my unfinished basement. I am going to be finishing it soon and I would like to "redo" some of the vent work, pipes, etc.

Sorry I don't know the proper wording but there is a big main section coming from the furnace and it splits into two and goes it separate ways ( I was already told this was bad that is too much work to fix). The one section I wish to change if possible is one section that runs the span of my basement and will make me substantially lower the ceiling in the section it runs and it is almost down the middle (can't believe it myself). I was wondering if it was possible to take down the large rectangular "box" and replace it with just 4" round sections which i could tuck up beside the main beam. It is the section that pushes the air upstairs to the second floor. It breaks down to a 4" section and the end if it to go upstairs so I am just going to be starting it sooner.

Hope that makes sense thanks for any help