When setting up travel agency contracts, if the travel agency charges VAT do I add that to the commission rate?

You do not need to include the VAT percentage on top of your commission. Regardless of whether your system is set on Net or Gross pricing, when you set up your rates, you apply VAT anyway. 

For example, if a travel agency commission is 15% and they say there is a VAT of 2%, then you only need to insert the 15% commission.

 

Note: The commission in the Reservation Report changes based on whether you display as Gross Values or Net Values, but always uses the same percentage from the TA Contract. If you want the commission on Net values, then display the report using the Net Values filter.

 

 

For more information on setting up travel agency contracts, check this article: Set up Travel Agencies

For more information on travel agency commissions, check this article: Travel Agency Commission