zaphod, from reading your posts I understand you don't want to use the NIOS processor, but you just want to access some SDRAM chips from your custom FPGA logic.
If this is true, then using the term "NIOS system" in your post is incorrect - you don't have any NIOS processor there. You want to call it "SOPC Builder module" or "Avalon switch fabric module" for example, because it's the logic automatically generated by SOPC Builder which contains the point-to-point Avalon bus logic between your (custom) master and peripherals (SDRAM controller in this case).
Now to answer your question: you want to perform a read-modify-write operation from your Verilog custom logic into the SDRAM.
You need to write your custom logic to be an Avalon master (refer to Altera docs on how to do this). Your custom master will have to handle the address generation and the wait states/latency of a generic Avalon slave (Altera docs tell you how to do this) - no need to delve into the intricacies of an SDRAM controller.
You can use Altera's SDRAM controller provided with Quartus/NIOS tools. Just create a SOPC Builder module and add these 2 components: Altera SDRAM controller, and your custom Avalon master. Make sure you hardcode the memory base address correctly in your master, or make it configurable. Generate the SOPC system and DONE!
Regarding the burst mode, Altera's SDRAM controller is not capable of burst mode access, you will have to switch to DDR, or buy an SDRAM controller IP from another company, or write your own
http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/smile.gif
Good luck!