Your CSV file must have the column names as the first line.
You can create split transactions with up to three splits. Splits must be separate columns (so each transaction still takes one lines), the column name must be the Category name for the split, and the column value for each transaction must be the amount of the split.
Date Description Amount CategorySplit1 CategorySplit2
2012-12-31 memo here 100.00 90.00 10.00
Load the CSV file, click the Review Mapping and assign the split columns on the sidebar at the bottom. Save the mapping and recreate the QIF file.