1. There is a potential for confusion here, in that there are two bodies of code available for Nios II which are both called the HAL. One is the Altera HAL provided with the Nios II development kit, and the other is the eCos HAL provided with the eCos port. They both perform similar functions in that they provided simple C runtime environments upon which operating systems can be built. However the API's are different for these two bodies of code.
In the case of eCos you should refer to the eCos documentation for the available API. From Redboot you can use the flash image system (FIS) API, or from an eCos application you could use either the romfs or jffs2 file systems. These file systems can be accessed using the standard file API's (e.g. mount(), read(), write() etc.). See the eCos reference manual for details.
2. If you set the startup type to "ROM" then you should also ensure that in SOPC builder you set the reset vector to point to the flash device you want to boot from. You may also want to point the exception address to point to this device as well. The location of the remaining code sections is defined using the drop down menus in configtool (eCos HAL->Nios2 architecture->text region etc.).