Assuming eduke32 is in the DN3D directory along with the HRP files (there should be a "highres" folder among other things) you should be able to run it and choose the "highres" content folder from the drop-down at the bottom of the launcher. If you've already set eduke32 to skip the launcher you will need to delete the settings file so it will appear again. The HRP has its own high-res title screen etc. so it should be immediately obvious whether it worked or not.

If for some strange reason this doesn't work run the HRP installer again, this time choosing to install eduke32, and then replace its outdated version with the latest build. It should then automatically inherit all the settings and everything needed for the HRP to work.