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This prevents run ins with the fabled "rescue squad"
There are a couple ways to know, is there a little ninja icon in your app list called "Superuser Permissions"? Also you could use a file browser like Astro or Root Explorer(which I would recommend to get the most out of a rooted droid) and see if it will let you navigate to the folder above your sd card(the root folder of your phone).
The way I get rid of bloatware like Amazon Mp3 is by using a file manager to go into /data/app then scrolling down and locating what you want gone and deleting(Be very careful here, this is the reason your phone doesn't come with root access out of the box)
Also now that you are rooted I would recommend making a backup in your phones recovery(sprecovery or clockwork) everytime you make a change to your phone. This prevents run ins with the fabled "rescue squad"
There is an icon named Superuser Permissions.....it is sort of a modified skull and crossbones icon though.
When you say a file manager....then go into data/app.......how do I do that? Do I need to "mount" the phone and access the folders that way?
Is there a way to get to the SD card any other way?
....to access the system folder you need to figure out how to use adb or buy root explorer (simpler IMO)
nothing else will let you modify the /system. this isnt on the sdcard just so you know.
Is root explorer on the app store?