Using otool -D lib.dylib returns the path that is presented by that library to the compiler. To change it you can use install_name_change with the argument -id.
install_name_tool -id “@executable_path/../Plugins/lib.dylib” lib.dylib
This alters the relative path of lib.dylib to the plugins folder of your bundle. Next you need to change each path in the main executable. You can find out the dependencies and their expected path of the executable using otool -L. For each dependency that needs changing use install_name_tool again with the argument -change.
install_name_tool -change “/usr/lib/lib.dylib” “@executable_path/../Plugins/lib.dylib” applicationname
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