How to map data from AutoQuotes Catalog Data Export to Magento Standard Products File to Import?

Question

I am creating an e-commerce website using Magento 1.9 platform and they ask me to take the products data from AutoQuotes Catalog Data Export (http://aqnet.com, and they provide a Windows application with authentication to access the user's database).

However, the CSV file which is downloaded from the software has many columns which does not appear in a standard Import File of Magento (and vice-versa). I just want to ask what is the best way to map those data because there are approximately more than 10,000 products or what is the best solution I can do in this situation?