i think i have found the answer to this question. In order to write to System folders you need to have permission to write on that folder. My app had a Daemon attached to it, so i had to copy that Daemon to /System/Library/LaunchDaemons to make that Daemon work. So as i am developing for JB iphone and people are going to install my app using Cydia, why not to make Cydia install the files of my app to proper locations. I made Cydia to copy the Daemon file into /System/Library/LaunchDaemon folder. Now the question is how Cydia will know where to paste the files. Answer is simple, just make the proper folders in .deb file and cydia will paste the files located in the folders inside the .deb file.
For Example if you have a Daemon and you want Cydia to paste it to /System/Library/LaunchDaemons , make the file structure like this before making a .deb
+- MyApp
+- Applications
+Myapp.app
+-DEBIAN
-control
+-System
+-Library
+-LaunchDaemons
+- com.myLaunchDaemon.plist
Cydia while installing your app will paste the com.myLaunchDaemon.plist file in System/Library/LaunchDaemons, reboot and you are good to go.