Configuring a part of cyclone II

No.

The internal parts of the FPGA are not user accessable in general.

You create internal structures via either a programming language (VHDL, Verilog, AHDL, OpenCL, etc) or schematic entry mentod, and the Quartus II software (synthesis - place and route) reduce that structure down to the logical gates and registers to represent your design intent.

That said, in future architectures, you will be able to do partial reconfigurations of the internals of the devices so that small portions (small if you define them to be small) can be replaced without changing the rest of the internals of the design. SAt the theoritical limit, you could define one LE as the smallest 'part' to be replaces, and thereby replace the location by loading that 'differential' programming file to the part.

This is not a capability of the Cyclone II family.

Regards.