you can fix wires in the programmer's connector, and stick the wires in the corresponding pins at the other end. it's a bit tricky to make a ISP6 male connector on a breadboard, so it's just plain easier to take the wires from the programmer individually and put them where needed.
that's the way I do it - Ii have a home built programmer and it doesn't even have a 6 pin connector, just individual wires for each signal.