A total fee is payable to the Danish Medicines Agency and the Research Ethics Committees on Medical Products (MREC) for the review of applications under the regulation. The fee is paid to the Danish Medicines Agency as described here:
Fees for clinical trials
Fees must be paid to the Danish Medicines Agency no later than one month after the invoice has been received.
Note that the fee is the same regardless of whether you submit Part I and Part II separately (at a time delay) or at the same time.