APL2 folder is iGO application folder contains all the map data, application executibles and other required files.
Data folder is for Pioneer menu files; XM files, wav files for system sounds, and etc files. You don't really need to update this folder but personally, I didn't like the original (v2.006) system sounds.
APL folder is main Pioneer applications and launcher (media player, parriot BT app, and etc). I tried to update to v3 but it didn't work (didn't pass boot splashscreen on second boot). I'm guessing it requires new WinCE to work properly. oh well, new maps and navi s/w is