Ardour will only ever deal with a single audio device. If you want to use more than one, you have 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. You cannot stop this drift, although in some cases the effects may be insignificant enough that some people might not care about them.

Thus in an ideal world you should not use multiple independent soundcards but instead use a single device with a single clock and all the inputs, outputs and other features that you need.

Of course, a lot of people don't live in an ideal world, and believe that software should make up for this.

OS X

In CoreAudio, aggregate devices provide a method to use multiple soundcards as a single device. For example, you can aggregate two 8-channel devices so that you can record 16 channels into Ardour.

If you are using a single typical 3rd party audio interface (such as those from Apogee, RME, Presonus, and many others), or you are using JackPilot or a similar application to start JACK, you do not need to worry about this.
You will need to set up an aggregate device only if either of the following conditions are true:

You want to use two entirely separate devices and want to start JACK using Ardour.
You want to use your builtin audio device and want to start JACK using Ardour.
You want to use more than two entirely separate devices

In the case of your builtin audio device, you will need to create an aggregate device that combines "Builtin Input" and "Builtin Output" into one device.

OS X

Linux