A site like Qhapaq Nan is fairly difficult to grasp. Is it the roads the Inkas built to connect all parts of their empire? Or does it refer to the sites the roads connect? Or a combination of the two? It doesn't really help that the nomination file comes in at 500 MB, the site names are somewhat cryptic IDs and that the GPS coordinates repeatedly do not match the nomination file boundaries. For a detailed discussion using Pachacamac as example, check Solivagants comments in the forum. 

To tackle the site I visited multiple points along my trip in Peru and Bolivia. You will find comments for each below. Personally, I would prefer the site to be limited to the actual trails instead of serving as a one size fits all nomination for Inka sites.

Pachacamac

Pachacamac is located South of Lima and a tentative site on it's own. It's here that the Qhapaq Nan reached the coast. Unfortunately, I was not able to find any remnants of the trail and the nomination file and the GPS coordinate took me into some random suburb wihere I was unable to spot any archeological traces. To get there grab a bus on the Panamericana heading South to Lurin.

Cusco

It's in Cusco that I actually found a trail labeled Qhapaq Nan including a sign. It's very well visible (see my picture) and starts near the Templo de la Luna/Chukimarka. The GPS coordinates we show are nearly correct. The trail runs North to Yuncaypata. My recommendation would be to visit Pisac first and on your way back ask the driver to let you get off at Yuncaypata. From the car window I saw the same Qhapaq Nan posting at -13,4883238, -71,9359134, so I would presume that's where the trail starts on the other side. From there it's a downhill hike back to Cusco.

The market square in Cusco supposedly was the nexus of the Qhapaq Nan and according to our connection Exact Locations inscribed twice (or more) should count, too.

Raqch'i

I took a tourist bus from Cusco to Puno with multiple stops in between, one being Raqch'i. The Qhapaq Nan runs right through it. Upon entering the site head straight for the map posted at the entry and you will see it. I would recommend ignoring in the tour guide and focusing your limited time on the Qhapaq Nan remains which are well visible here.

Tiwanaku

The Qhapaq Nan is also marked for Titwanaku. I didn't see any remains, but well. Again a site that counts twice.