thanks to cktricky for pointing me to:
Once you've gotten it installed/unzipped its fairly easy to use. Download your .apk from the emulator.
user@dev:~/android-tutorial/android-sdk-linux_86/tools$ ./adb pull /data/app/com.joelapenna.foursquared.apk com.joelapenna.foursquared.apk 2441 KB/s (625416 bytes in 0.250s)
From there simply decode the .apk
user@dev:~/android-tutorial/reverse$ ./apktool d com.joelapenna.foursquared.apk foursquare
I: Loading resource table...
I: Decoding resources...
I: Loading resource table from file: /home/user/apktool/framework/1.apk
I: Copying assets and libs...
From there you should have a folder looking something like this
inside your smali folder will be all the decompiled java. have fun.
actually after i did the above, I found this which is a video covering the above and previous posts.