Re: problem with nm-applet
nm-applet is one of the 2 parts for network-manager: Network-manager daemon and the applet. To be able to interact with daemon the user needs the applet, and user need to belong to netdev group..This is in a very general way the way it works. For more details please read the "man NetworkManager".
According to the error, the applet is already running..Make sure it is running before running applet again: use the command ps, I always use it, in your case use ---> ps -axjf and look for the gnome info in the tree the nm-applet...It must be under the gnome section.
Looking at the second paragraph, you are starting a script...I think you are little confused....You modified the interfeces file, then run the network-manager, then applet?..
You can just run: /etc/init.d/networking start|stop and try to run ifup (it reads the /etc/network/interfaces) to configure interface.
This is what I understand from you..Correct me if I'm missing something or missunderstanding the issue. I'll be glad to help..