I am a Linux n00b. I only really started looking into Linux properly yesterday when I downloaded Back Track but I think I have learnt enough already to answer your questions.
Firstly you need to give more info...
What GUI did you load uP?? There are different wireless tools in each.
I found I had to use the KDE GUI as this was only one that had a wireless config utility that allowed me to type in my WPA details. The Flux GUI only support a WEP hex key (as least that is all I have found so far).
If I Have read your post correctly you are saying that when you type ifconfig wlan0 down it tells you need to install aircrack??
I can't see how this would happen as I thought IFconfig is a built in command to the Linux OS that allows you to configure WIRED interfaces so why would this rely on aircrack?
Also, what version of back track are you using. Mine was back track 3 in which I am giving my examples from.
As I said I am a complete n00b so I may be wrong about the above but I would find it quite strange if you did need aircrack to use the ifconfig command...