If the original is in 2 or more columns, then it is using HTML tables. Most eInk readers are too small to deal well with HTML multicolumn tables. Trying to convert HTML tables by hand is a tedious task. However, if you convert the tables to epub hen use the Sony Reader's column function it might look okay. Have you tried that?

EDIT: I just went and looked at the website you wanted to read on the reader. Forget it! That kind of website will never look good on a small eInk reader. You might be able to copy the text from the center column and paste it into a program to create an epub or some other convertible format, but the two side columns will never look good.