The main diff between Temp and Perm root, is that you can delete system files with Perm root, which allows you to get rid of programs that are installed on your phone that you don't want there. There are many other advantages, but I think that is the biggest diff that I can see. Both Temp and Perm root give the ability to run root only type apps.
Currently I have Temp root using Visionary 13 (14 never worked for me not sure why). I have it set to root if at any time the phone reboots or I turn it off.
Once I decide to do so, I'll perm root the phone so I can load different ROMs, which if what I'm reading on the forums, is not something you can really do with Temp root (someone will correct me if I understand that bit wrong).
Perm Root is not something you want to do if you are the type that worries about voiding your warranty or does not understand how to un-root your device.
In either case, make sure you have downloaded everything you need to root BEFORE you start. And follow whichever method you plan to use FULLY step by step without skipping any steps, unless you know those steps actually can be skipped for your device/version of OS that you currently have on your phone.