As of the next pre-release (probably 6.0.8) a bunch of terms are being changed within the product to promote ease of use and understanding. Note that these new terms will not make it to the online documentation immediately.
Old Term --- New Term
Instrument -- Output
Instruments will now be called outputs. The term 'Instrument' has been antiquated ever since the bank and program fields were added to the product. Also in this next pre-release, audio input (for multi-track record) is no longer selected from the output ('instrument') so there is no longer a connection between the old term 'instrument' and audio inputs. All audio inputs will be selected from the audio record input select field of the tracks window (accessible from the down pointing triangle). This also makes it possible to use all of the inputs on audio cards which have more inputs than outputs.
Instruments -- Mixer
The instruments window is now called the mixer window as this is the term musicians are more familiar with.
More discussion can be found here:
http://sagantech.com/metroforum/viewtopic.php?t=253