I will try to cover two cases: updating from Cloud Controller (applies only to partners who has a separate Cloud Controller) and updating from MyStandard page.

MyStandard:
At the current moment it's not possible to do halcust updates when updating version. You by default the server will keep the same halcust/halpatch for the new version. In coming weeks we will add option to upload halcust/halpatch just before update.

Cloud Controller:
1. In the server folder you need to create a folder newver.XXX, where XXX is the version code of the version you will update the server to. For example, newver.STDSVR_8.3-2017-01-08-0011
2. Put the new halcust and halpatch in the newly created folder.
3. In the remote cloud server record you need to set Halcust Update and Halpatch Update radio buttons to values "Use Updated"
4. Perform the server update function.