Thanks again Ted,
I now have this working as wanted. I've put the .ipx file in the sub-component folder, and it points to the next folder down where the .qsys file is for the sub-component, and also added the path for the sub-components IP folder. It means that I've now got an extra folder level for the .ipx file, but it seems to work very well. I haven't tried it yet, but I expect that this would allow multiple levels of hierarchy to be nested.
I still think the paragraph at the bottom of page 7-9 on the link you sent me is a bit misleading, as it seems to indicate that .qsys files wouldn't be picked up. Maybe Altera could update this at some point.
Thanks again for all your help,
Mark