Thanks Hans. After some searching in the test suite I found the answer, which I'll put here in case someone else is searching for it, which is:

\setuphead[section][sectionsegments=section]

\setuphead[subsection][sectionsegments=section:subsection]

which sets up sections to just be numbered with the section number instead of the part, chapter and section number, and sets up subsections to just be numbered with the section and subsection number.

Now that I know how to do it I see mkiv is much cleaner on this code and the change gets reflected in tables of contents etc. This was much harder in mkii. Thanks again.

Duncan