Hi,
I have not worked with Max Plus II. But I am assuming that the navigation flow may be different, although the functionality may be the same. Can you clarify what exactly you want to do? What do you mean by "writing a file to the Altera?". If you want to program the Altera FPGA with the system that you compiled using Quartus II, then click on Tools Menu then click on Programmer. Then you can select JTAG or AS mode as per your requirements and program the device using Quartus II Programmer. You can refer to "About Programming" in Quartus II integrated Help System for more details about the programming files and methods.