If the Commission sets the status of the ACR as 'EC Assessment with observations' you have to reply uploading the document 'MS Reply to Commission observations' in the ACR.
This document is a non-integral one, so you can upload it at any time to the EC once the ACR is sent (for registration of these non-integral documents we need to know the Programmes covered by this ACR and this is only known and stable after the ACR was sent to the Commission).
Go to the Documents section (1) and click on the 'add' button (2) select the 'MS Reply to Commission observations' document (3), when you finish to enter all the information click on the 'Update & Send' link (4) to send it to the EC:
If the Commission sends you more than one 'EC Assessment with observations' for different ACRs, you have to upload your reply as 'MS reply to Commission observations' in each of the ACR.