Specifying multiple memory segments for code or data to linkers is a normal capability, so I expect it is true also of the gnu linker. However the NIOSII IDE presents a simplified interface since it only allows a single selection in the .text memory drop-down list. So unless you create your own linker script the only option seems to be to specify sections using __atttribute__ (NIOSII software manual page 4-32). That's not very satisfactory from a maintenance/portability point of view. Maybe Altera should consider allowing multiple selections, or address the original problem of allocation granularity.