As long as all the combinations have the same product ID then it will match the combinations to the same product. So if you have a T-Shirt from Small to XXL in black and white, the columns for Product ID, Combination Ref, Product Name, Combination Name and Combination Value would be as follows:
1000, 1000-1, T-Shirt, Size;Colour, Small;Black
1000, 1000-2, T-Shirt, Size;Colour, Medium;Black
1000, 1000-3, T-Shirt, Size;Colour, Large;Black
1000, 1000-4, T-Shirt, Size;Colour, XL;Black
1000, 1000-5, T-Shirt, Size;Colour, XXL;Black
1000, 1000-6, T-Shirt, Size;Colour, Small;White
1000, 1000-7, T-Shirt, Size;Colour, Medium;White
1000, 1000-8, T-Shirt, Size;Colour, Large;White
1000, 1000-9, T-Shirt, Size;Colour, XL;White
1000, 1000-9, T-Shirt, Size;Colour, XXL;White
Even if you have 100 combinations for one product you just continue like this and can easily add them all in minutes.
All the combinations need to be together in one field separated by a semi colon as in my spreadsheet.