I am using a laptop equipped with Windows 7, Finale 2012a, and Virtual Drumline.  The NanoKey2 is my input device.  I have put in the sounds for the different layers that I am wanting and even attempted to apply the midi maps that Virtual Drumline has available, but two issues occur:

1) When I play the unpitched sound on my MIDI keyboard, the desired sound plays back accurately but is notated incorrectly with disregard to the percussion map.

2) When I go back to the original layer (pitched) there are random pitches that will not play back from my midi keyboard. 

I must be doing something wrong here!

Virtual Drumline doesn't come with any sort of specialized Finale midi maps. The easiest way to integrate VDL within Finale is to use a template package from [url=http://www.thewritescore.com]The Write Score[/url].

If you're already using one of their templates, you may want to see if the documentation addresses this, or perhaps try asking them for advice if you're getting stuck in the process of implementing your Finale template

The best solution is to use the Change Instrument Utility rather than Layers. The notation setting found in the lower right corner of the Score Manager is for the entire staff and not independent for each layer.