Would these be system files or files you added to the phone?

For added files, the only requirement for notifications and ringtones is that they are in a folder called 'notifications' and 'ringtones'. You can have them nested in other folders and you can have multiples, but it tends to confuse the system if you have the same ringtone file in multiple ringtone folders.

As to the reason why, remember, you asked ....

Newer phones and Tablets that include large amounts (by current mobile standards) Like the SGS2 (and my other phone, the Captivate) often partition them so that you don't have a huge amount of system memory that wouldn't be accessible for file storage. On the Captivate (and I am assuming it's similar with your device) Samsung has a 2 GB partition for the system and the remaining 14 GB partitioned and recognized as an sd card by making its mount point /sdcard.

Therein lies the problem. The path to external storage within Android is /sdcard so apps that are installed to external storage will be there, which is the internal sd partition, not the removable sd card. On the Captivate the path to the removable sd card is /sdcard/sd_external, on my SGS2 it's /sdcard/external_sd and on my Transformer is /Removable/Microsd. Custom roms can mount the external card anywhere. Check with the developer for the mount point if you can't find it.

If you have an internal sd card partition, then that will always be the default location for files, apps and data to be stored as defined by the mount point /sdcard. If the phone has no sd card partition, then an external sd card will mount at /sdcard when inserted.

 

They would be in system folders. Without root you won't be able to see them.

 

Wallpapers can reside anywhere, as long as they are a format your phone can read. The audio files you are correct. The general convention is to put them in the following hierarchy on your /sdcard partition.

/sdcard/media/audio/alarms
/sdcard/media/audio/ringtones
/sdcard/media/audio/notifications

But that is just for organizational purposes.