You can get an overview of the transfers you have to do manually by clicking on the salary period and then clicking on Overførsler.
If you want a complete overview of all transfers, go to Virksomhed -> Overførsler.
Salary: Will be paid to the bank account belonging to the employee. The payment will happen on the disposition date (this can be found on the payslip).
Skat (and AM-bidrag): Transfer this to the Skattekonto. Read more about this here: http://skat.dk/skat.aspx?oid=2234894
It’s not possible to manually transfer ATP. In order to pay ATP (in the right way), you need NETS. If you don’t have NETS, you’ll receive a reminder from ATP - you will be able to pay that.
Read more about ATP here: https://indberet.virk.dk/myndigheder/stat/ATP/Se_indberetninger_og_indbetalinger
It’s not possible to manually transfer holiday pay. In order to pay this (in the right way), you need NETS. If you don’t have NETS, you’ll receive a reminder from Feriepenge - you will be able to pay that.
You can read more about payment of holiday pay here: https://indberet.virk.dk/myndigheder/stat/feriekonto/Betalinger_og_indberetninger
The best to do here is simply to talk to your pension company. Every pension company has its own way to handle manually payments.