Ardour will only ever deal with a single audio device. When it is desired to use more than one audio device at the same time, there are two choices:
Ardour is fundamentally designed to be a component in a pro-audio/music creation environment. Standard operating practice for such setups involves using only a single digital sample clock (something counting off the time between audio samples). This means that trying to use multiple independent soundcards is problematic, because each soundcard has its own sample clock, running independently from the others. Over time, these different clocks drift out of sync with each other, which causes glitches in the audio. This drift cannot be stopped, although in some cases the effects may be insignificant enough that they might not be noticeable.
Thus, in an ideal world, a single device with a single clock and all the inputs, outputs and other features needed should be used. Of course, there are those who like to point out that this is not an ideal world, and believe that software should make up for this.
In CoreAudio, aggregate devices provide a method to use multiple soundcards as a single device. For example, two eight-channel devices can be aggregated so that 16 channels can be recorded in Ardour.
When using a single typical 3rd party audio interface (such as those from Apogee, RME, Presonus, and many others), or using JackPilot or a similar application to start JACK, there is no need to worry about any of this. An aggregate device only needs to be set up if any of the following conditions are true:
In the case of a builtin audio device, an aggregate device that combines "Builtin Input" and "Builtin Output" into one device needs to be created.
The precise instructions for creating an aggregate device on OS X have varied from one released to another. Please read https://support.apple.com/en-us/HT202000.
Please see the instructions at http://jackaudio.org/faq.