Thanks sstrell, I understand now.
On a similar topic, I've managed to fit my design onto the economical version of the nios ii, but despite generating a .jic and uploading successfully, I still need to start the nios ii on every startup from eclipse (run as hardware). Is there a way I can get it to run on startup with my free licences? Or would I need to purchase something from Altera?
If it is possible without purchasing what is the procedure as I have tried using the NIOS ii flash programmer but it seems to refuse to cooperate, even when I tell it to ignore mismatched system ids etc. See below.
Many thanks in advance again.