For most cases, you never touch the AT column. If you are making variables for inputs and outputs, they are assigned on the I/O Map screen. You can see what connection is assigned by reading the text of the AT column, it will show the connection point for the data. This applies to the local and networked devices.
You can however still force old fashioned Omron PLC addresses, and that is really only used for backward compatibility with an HMI or data collection product that cannot import the variables. As an example, if you want to store an integer value to D0, you would create a variable and then set the AT column to %D0. This is absolutely a backward compatibility thing, and is not required in order to properly use the PLC. In fact, I believe in some of the newer PLCs, you actually need to go into parameters and enable those memory addresses if you intend to use the old style.