How to set properties of a line connecting two blocks

I am writing script to build model by command line. I have learnt how to set position for each block, but when I have to connect more blocks to the same side of another block, connections are not so nice. So I would like to know if there's a way to modify connection points. I have attached two images: - 1: it shows as it is now - 2: it shows as I would like it to be

Thanks

http://oi43.tinypic.com/907tdl.jpg

http://oi39.tinypic.com/14y1v7m.jpg