question related to DE4

No, you should not put the project files under that path.

You just need to tell Quartus where it can find ModelSim.

By executables, I mean "vsim.exe" and such files.

I don't have ModeSim for Windows at hand, so I can't really tell you which folder it is.

ModelSim is a simulator. Quartus performs the actual synthesis.

If all you want to do is VHDL/Verilog behavioral simulation, ModelSim is all you'll need.

But if you intend to load your design into a FPGA, you need to use Quartus to synthetize the design and produce the configuration files. You should also learn about TimeQuest for timing constraints.

Quartus also produces a gate level model of the synthethized design which you can load in ModelSim to perform a gate level simulation.