How do I rename machines?

You can open the Machine Details and on the Operating System page you'll see the Machine Name. If you change this then the next time you scan the network it should pick up a "new" network connection (matching on the remote name for the network connection) but it will be intelligent enough to realize that this corresponds to an existing machine on the network (matching against the machine name) and so rather than adding a new machine to the inventory it will update the "Remote Name" for that machine on the network and then compare the latest audit to the configuration items that are currently stored in the inventory database (raising alerts for any faults or changes). 

The auditing engine is basically designed this way to handle IP Subnet scans where a machine may have more than one network card and/or IP address on the network or where the IP Address might be allocated by a DHCP server (and subject to change) - but this will work for Domain networks that you have defined as well. Essentially the machine name (which is a property of the machine itself, and which you can edit in the Operating Systems page of the machine details) is used to identify the machine on any given network and the Remote Name is the machines pingable address on the network (be it IP, simple name or FQDN).