There is a 'Filters' tab in the extension which is available for opencart versions 1.5.5 and newer. The tab lists all available product filters there. If the product belongs to the filter then you can import an option for the product there.
The cell can contain more than one value for the filter. In this case they are separated with the general separator (':::' - default). Here is an example for the 'Color' filter.
model,...,filter:color,....
PROD1,...,"green",...
PROD2,...,"green::blue:::yellow",...