If you used home-brew to install RDkit as described here updating is very simple

brew update
brew upgrade rdkit

You can check which version you have installed using

MacPro> python
Python 2.7.11 (default, Dec 23 2015, 16:11:50) 
[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import rdBase
>>> print rdBase.rdkitVersion
2016.03.1
>>>