MFDeploy can be used for monitoring and debugging by displaying debug messages. In your program code include statements like

 Debug.Print("Some message of interest");

Make sure your .NOW is plugged in via USB. Using Visual Studio, deploy your solution to the device. Then open MFDeploy and choose the device. Next, connect to it by clicking Target -> Connect (or press F5):

You may need to press the Reset button on the .NOW to get the program started. Once started, you'll see messages appear in the window:

If you have two or more .NOWs connected, you can open multiple instances of MFDeploy and connect each one to a different mote.

You can only connect a .NOW to one host program at a time. This means that you can't be connected with MFDeploy and at the same time use Visual Studio to deploy a solution. In MFDeploy use Target -> Disconnect (or ctl-F5) to release the connection. Then you can deploy using Visual Studio.