Is it possible to load a small custom bootloader

Alex: EPCS16 & 64 should be supported by the flash programmer in the next Nios II release. If you need something sooner (I know several people have mentioned trouble here on the forum) let me know and we can work something our in the 'untested IP' section.

Ken: Currently we only support CFI-compliant flash and the EPCS (serial) flash devices for booting Nios. To be honest I am not very familiar with the EPC-series of devices. I do know that they have been used with Nios systems in the past, though. I would imagine that once the physical flash interface is worked out along with a programming method, the boot-loader could be ported over from our CFI-flash boot-loader easily (off the top of my head I cannot think of any significant changes required to it). The CFI boot-loader basically requires that you program in the .flash we create for you based on the project .elf (as this contains the address/data records that tell the boot-loader where to place things in memory). The boot-loader assembly source is available in the nios2/components/altera_nios2/sdk/src/boot_loader_sources folder -- look for the "cfi_bits" source file.