I have found the following two sites explaining how to setup Python Virtualenv for ArcGIS:
- ArcGIS and Virtual Environments part 1: ; ArcGIS and Virtual Environments part 2:
- Calling arcpy from an external virtual Python environment:
I've successfully created a virtual environment under my external drive:
- E:\Python\Venv\ArcPy64bit

When I followed the second part of ArcGIS and Virtual Environments part 2: as well as Calling arcpy from an external virtual Python environment: to create the Python Path file to the ArcPy and my ArcHydroTools is where the comes apart.
As instructed I ran the following within my Python IDLE:
import sys
sys.path

I then created the Python Path file from the list above:

I copied the path file (arcpy64bit_paths.pth) under the following directory:
- E:\Python\Venv\ArcPy64bit\Lib\site-packages

When I setup the Python Interpreter using the virtualenv within Eclipse the following paths are recognised:

ArcPy and ArcHydroTools not recognised:

When I setup the Python Interpreter using the ArcGIS Python within Eclipse the following paths are recognised:

ArcPy and ArcHydroTools are recognised:

Any help to resolve the following will be appreciated, as I really need to use virtualenv to manage my Python Environment due to different versions of packages required.