NEEK on board USB blaster

I don't have a neek schematic to hand so can't check it to confirm what you say. There certainly needs to be a a way of disconnecting the TMS and TDO pins between the On-Board USB-Blaster and the Cyclone.

If you can achieve that then the next issue which may cause you problems is that most of the On-Board blasters are set up so that they disable themselves when a cable is plugged in. One of the ground pins has been re-purposed as a sense pin to make this happen. Disconnecting the sense pin from your cable will avoid this, but take care because if you get this wrong you might fry the On-Board blaster on the NEEK board (or the other board, that one must have the sense pin connected to ground).

The final issue you'll face is that you need to have a good quality short cable between the boards to get the needed signal integrity. 10MHz signals don't go down a standard ribbon cable very far before they are degraded beyond use.