We were waiting for it for over a week, the update is finally available. Cydia Substrate updated to version 0.9.5000 and is compatible with iOS 7 but especially with the A7 chip with 64-bit. Now the tweaks that developers have compiled to 64 bits will work on the iPhone 5s, iPad Air and iPad mini with Retina display. Expect a wave of tweaks and updates.
So, as explained by Saurik, the tools that have been updated to support iPhone 5s and iPad Air and iPad mini 2, will work normally on these devices, and the tools that have not been updated to support these devices won't, so you must wait for their developer to update them to support A7 processor.
Note that some tweaks won't work as expected, so you should remove them then install Cydia Substrate then reinstall them.
