No matter what, whenever you run python from within ArcMap or ArcCatalog it will be using the 32 bit Python (C:\Python27\ArcGIS10.1). The 64 bit python IDLE can only be used as a stand alone script outside of ArcMap/Catalog, therefore, when you try to import modules from the ArcGISx6410.1 folder the modules will not be found. If you want to use scipy in the Python Window inside ArcMap, you must install the 3rd party module in the "C:\Python27\ArcGIS10.1\Lib\site-packages" folder as well.you can Check where your PYTHONPATH is with a simple test:
>>> import sys
>>> for pypath in sys.path:
print pypath
C:\Windows\system32
C:\Python27\ArcGIS10.1\Lib\idlelib
C:\Windows\system32\python27.zip
C:\Python27\ArcGIS10.1\DLLs
C:\Python27\ArcGIS10.1\lib
C:\Python27\ArcGIS10.1\lib\plat-win
C:\Python27\ArcGIS10.1\lib\lib-tk
C:\Python27\ArcGIS10.1
C:\Python27\ArcGIS10.1\lib\site-packages
C:\Program Files (x86)\ArcGIS\Desktop10.1\bin
C:\Program Files (x86)\ArcGIS\Desktop10.1\arcpy
C:\Program Files (x86)\ArcGIS\Desktop10.1\ArcToolbox\Scripts
>>> # To see what version of Python you are running use:
>>> print 'Running against: %s' %sys.version
Running against: 2.7.2 (default, Jun 12 2011, 15:08:59) [MSC v.1500 32 bit (Intel)]
>>>
How can I configure Arcmap to search for the 64-bit 3rd party modules in C:\Python27\ArcGISx6410.1\Lib\site-packages
You cannot configure ArcMap to search these 64-bit 3rd party modules because ArcMap can only use the 32 bit Python. Therefore, you must use the 64 bit IDLE whose paths are in the C:\Python27\ArcGISx6410.1 folder.Here is my 64 bit PYTHONPATH:
>>> import sys
>>> for pypath in sys.path:
print pypath
C:\Users\GIS\Desktop
C:\Python27\ArcGISx6410.1\Lib\idlelib
C:\Python27\ArcGISx6410.1\lib\site-packages\setuptools-0.6c11-py2.7.egg
C:\Windows\system32\python27.zip
C:\Python27\ArcGISx6410.1\DLLs
C:\Python27\ArcGISx6410.1\lib
C:\Python27\ArcGISx6410.1\lib\plat-win
C:\Python27\ArcGISx6410.1\lib\lib-tk
C:\Python27\ArcGISx6410.1
C:\Python27\ArcGISx6410.1\lib\site-packages
C:\Program Files (x86)\ArcGIS\Desktop10.1\bin64
C:\Program Files (x86)\ArcGIS\Desktop10.1\arcpy
C:\Program Files (x86)\ArcGIS\Desktop10.1\ArcToolbox\Scripts
C:\Python27\ArcGISx6410.1\Lib\CalebsTools
>>> print 'Running against: %s' %sys.version
Running against: 2.7.2 (default, Jun 12 2011, 14:24:46) [MSC v.1500 64 bit (AMD64)]
>>>
You can always see what version of python you are running with:
import sys
print 'Running against: %s' %sys.version
I hope this helps!