I'm a little surprised that you created the bootloader so quickly. Makes me wonder if you missed something. Let's assume you didn't though.
By default, the EPCS controller peripheral in the SoPC system contains a block RAM. This block RAM contains the bootloader. That is why setting your NIOS processor's reset address to the address of the EPCS controller works.
That bootloader that I wrote is meant to replace the bootloader that is inside the RAM in the EPCS controller peripheral. If you are going to do it the same way you need to find some way to get your compiled bootloader into that RAM in place of the default bootloader.
I'm going to suggest a way of doing this that I actually haven't done yet but I think it will be easier for you.
Look in the folder where you've generated your SoPC system. You should see a file named something like "epcs_controller_boot_rom.hex". Your name might be different if you named your EPCS controller component differently. That ".hex" file contains the compiled bootloader that goes into the RAM block. Quartus compiles it into the FPGA image during assembly. You need to overwrite that file with your own compiled bootloader.
1 - Compile your bootloader.
2 - Create a .hex file (or .mif) file out of your .elf file and name it the same as the one being used by the EPCS controller.
3 - Copy your ".hex" file over the top of the old one.
4 - From Quartus run "Processing->Update Memory Initialization File". When that completes run "Processing->Start->Start Assembler". (If you have Smart Compilation enabled for the project you should just be able to hit the compile button and it will automatically determine just to do these steps). This will create a new SOF file with your bootloader in the EPCS RAM block.
You'll need to keep an eye out to see if/when your bootloader gets squashed by the other one (I assume it's going to be regenerated at some point). If you want to avoid this, I can suggest another method that may be slightly more complicated. It's basically telling Quartus to use a different ".hex" file to initialize that RAM block instead of the original.
Jake