My tube was flat in some parts of it, is there a way to make it more round so the liquid smoothly flows thru?
I think that was the reason I was seeing air bubbles in the tube.
You're seeing air bubbles in the tubing because you're letting air in it somewhere (connections are the most likely place). If this is the typical vinyl tubing that I think it is, just get some more. Seriously, my local big box home improvement store sells 20 feet of the stuff for less than $8.
You should replace if from time to time anyway.