The Automap MIDI client was introduced into Automap Universal 2 to accommodate the Nocturn, as the Nocturn has no other way to send traditional MIDI messages.
The Automap MIDI Client is designed to allow Automap users to send and receive traditional MIDI messages via the Automap Server. For many users this is a feature that may not be needed, as it is already possible to control most DAW software and plug-ins via Automap Universal or using the manual templates on the ReMOTE SL/ SL Compact.
Automap enabled plug-ins communicate with the Automap Server using Automation messages, this is how the learn function works, and why certain plug-ins (Spectrasonics Atmosphere for example) do not work well with Automap.
The Automap MIDI clients learn function works using traditional MIDI messages, and will only work with devices and software that send MIDI CC messages when a control is moved. This is very useful if you have a hardware synthesiser or sound module that you wish to create a 'MIDI control map' for, and control using Automap. However, although some software applications (Ableton for example) will send MIDI controller data when controls are moved, most plug-ins and other DAWs will not send MIDI data when a control is moved, hence the learn function will not work if the Automap MIDI client is being used to control them. For software and hardware that does not send MIDI CC data, and that can't be controlled via Automap, you will need to assign controls in the Automap MIDI control map manually as you would when creating a manual template.
The "Automap MIDI " MIDI port is a virtual MIDI driver which communicates between the Automap Server and any software that allows MIDI inputs and outputs.
If you want to use the Automap MIDI client to control an external hardware device you will need to assign the MIDI input and output of the Automap server to the physical MIDI port that you have the device connected to.
The use of the Automap MIDI client with the SL is explained in the ReMOTE SL Manual on pages 37 and 38, this can be downloaded from here.