I am not sure on the files layout of the "Edison SDK". You would need to check the layout matches.
If you are using the cross compiler within the Eclipse IDE from https://software.intel.com/en-us/iot/getting-started you'd get a cross compiler integrated into Eclipse.
Here you can definitely just extract / overwrite.
Hope that helps
What I'm unclear about is 'iotdk-ide-win' versus 'edison-sdk-win64-weekly-68'.
'iotdk-ide-win' is at your 'Setting up Eclipse' page which is part of your 'Getting Started for C/C++ (Eclipse) - Galileo & Edison'.
It's the full package to install the Eclipse SDK and works great.
'edison-sdk-win64-weekly-68' is on your 'Edison - Software Downloads' page 'https://communities.intel.com/docs/DOC-23242'
This contains a 'sysroots' folder apparently for the purpose of updating by overwriting the above SDK 'sysroots' folder.
It also contains these files:
relocate_sdk.py (I'm especially curious about this one)
I can't find any information about using these 'edison-sdk-win64-weekly-68' files. Also how can I be sure these files are newer than those in 'iotdk-ide-win' ?
To sum things up, what is the purpose of 'edison-sdk-win64-weekly-68' on your Software Downloads page?
Tbh I haven't checked details on the edison-sdk-win64-weekly-68 but I'd guess it's a cross compiling environment which you can use to compile for the target Edison.
iotdk-ide-win has a similar scope but it includes the cross compiler within an Edison environment.
The cross compiler itself probably is pretty similar (modulo probably a different set of libraries included). The Eclipse integration is only on the iotdk-ide-win.
Hope my view is correct and it helps clarifying