Hi Drinkyfish,
Unfortunately I did not reach to a solution for this problem yet!
Regarding setting the offset, it is one of the modification that you have to made, however it is not the only one, there should be some modification in the C code that is responsible of "reading" and "writing" to the ecps (this part I did not work on it yet)
Regarding the 2kb size, I also face this issue, however it does not make a sense! because the smallest epcs is 2MB.....but I do not know why it show 2kb
In order to find the base address and offset for the epcs, do the following:
1- From the flash programmer --> select New--> select the sopcinfo file
2- Under epcs_controller tab --> add the zip file --> after that you can see the base address and offset. (see picture 01 in the attachment)
3- Now right clich on the component folder --> Nios II --> BSP Editor --> select "Software Packages" tab
4- Fill here the base address and offset accordingly (pic 02 attached)
Good luck in your work and update me with any news!