Hi Abhay,
You will want to review the document below, but upgrading from 5.0.1 to 6.0.1 is a very smooth upgrade.
Always backup your existing deployment first.
The doc has step-by-step instructions on upgrading.
I suggest you read carefully and familiarize yourself with the new features and the differences between the releases before you upgrade.
There is ample information on every facet of Splunk and you should not expect any changes in the data at all.
There are however, vast changes in the interface and vast changes moving forward in how the indexes are handled so you will see improvements in efficiency across the board.
http://docs.splunk.com/Documentation/Splunk/latest/Installation/HowtoupgradeSplunk
With Splunk... the answer is always "YES!". It just might require more regex than you're prepared for!
