I created an application and a plugin, I want to create a package to be able to install both in another machine. I created a Package with "PackageManager" application. I added my plugin and my cocoa application. The "Destination" for my application is "/Applications". The problem is when I run my package it is not adding my application into "Applications" folder. If I change my destination to another root it is working. Any Ideas?
Do you have "Include root in package" enabled for the package's contents? See this answer for an explanation of what it does and why you probably need it.
Another possibility is that you have "Allow Relocation" enabled for the relevant components, so if they're already installed someplace else it updates them in place, rather than installing them in the expected location. This is usually (well, often anyway) a good thing, but it can make testing the installer confusing.