The eMote .NOW comes with two serial COM ports, COM1 and COM2. COM1 is primarily used to monitor system messages and Debug.Print output via a Serial-USB interface. This is what you're using when you have MFDeploy connected.

COM2 can be used for input and output via the screw terminals on the .NOW. A typical application would be used to connect a .NOW with another device such as a terminal emulator. Or, you could use it to communicate between two .NOWs. To use COM2, first look at your board and inspect the region highlighted in the image below. Each of the solder pad pairs (such as the two for R40 towards the bottom) should not have anything connecting them. If there is, use a soldering iron to melt the pads and tweezers to remove whatever is there.

To connect a .NOW to another device via COM2, you'll use the following pins:

Pin J11/5 doubles as a GPIO and as COM2 transmit, depending on how it's initialized in your program. When you create a SerialPort object on COM2, it becomes a COM2 pin. Similarly for J11/6, COM2 receive. Here's an example of how to connect two .NOWs. Note that J11/5 of each is connected to J11/6 of the other. Ground is wired in common between them.

When you write a program that uses COM2, you might find that nothing is happening on the serial port. The probable reason is that you are using the Visual Studio debugger or the eMote .NOW is attached via MF Deploy. In both those cases, Micro Framework (upon which eMote is built) automatically rounts ALL serial traffic to COM1. Hence when you run the program, you cannot use the debugger or MFDeploy. If you want to monitor the system and output from COM1, you can attach via a terminal emulator such as PuTTY. You'll configure the connection as Serial, provide the COM port used by Windows, and set the data rate, stop bits and protocol according to how you've defined the SerialPort in your eMote program.