Thanks Dave for the notes.
That's a little confusing for me (note 1 in the altera doc, I can only guess that 'configured for isp' means entering the programming mode). I'll just treat the JTAG port as if it's always a JTAG port then, and double-up the JTAG connections to spare IO (which I have heaps of) and be done with it - easy!
PS, no I don't want to reuse the header - in fact I want to get rid of the header & connect some uC IO to the CPLD with the same uC IO doing JTAG-y stuff as well as mode selection for my user code.
I think I'm sorted now though.
Cheers,
Doug.