How to avoid overlapping of Rapahel js path

Question

I have a flow chart which is based on Raphael js. it is same as that of http://raphaeljs.com/graffle.html. however since i have many rectangular Raphael boxes and my line path is of straight line and NOT curvy as shown in the above example. In this straight line type, these lines overlap sometime and so it is hard to tell which one is connecting which boxes.

Please let me know if i can achieve this and how.

Update :Attaching my current flow diagram jpeg. as you can see that connector lines are crossing over the Raphael shapes and also it is very hard to tell from where lines are starting.