Just have separate columns for Shipping vs Billing. Then under the addresses section in the mapper, click the + twice to create 2 address records (will show 2 rows as address1 & address2). Map the Shipping columns to the first record. Map the Billing columns to the second record.
Make sure that in the CSV file, the Label of both addresses is not the same.
In the Field Mapping section of the Import Assistant, For the billing address, map the Default Billing Address and set it to Yes, and map the Default Shipping Address and set it to No. For the Shipping address, map the Default Billing Address and set it to No and map the Default Shipping Address and set it to Yes.