nios -e is the economy version of the nios cpu, the smalest type.
you will need to open your sopc builder and change your nios cpu type from fast or standard to economy. this is also the slowest cpu type but it is free with quartus 9.1 and does not lead to a time limited design.
with quartus 9.1 the -e type is free and the first one you can programm into epcs or flash devices without a license, prior to quartus 9.1 you wount be able to generate files that can be used
in other words, if you want to store your design into non volotile memory to let it run directly after power up, you must use quartus 9.1 and the smalest nios or use a license.
sorry, i didn#t understand what you mean with another sof generated with quartus 9.0.
is it the same design or a different one like an example ?