Export EU B2C - Brexit

Good afternoon, 

I have the following question. 

We sell goods to EU consumers B2C. We have been charging VAT on our invoices. However, we send the goods through DPD and we receive an invoice for the cost of transport and another invoice for the VAT charges and we have to pay it to DPD. 

Is this correct way? 

How do you record this VAT paid to the courier on sage?

Any help would be grateful.