[FF44]

Specifically, do I delete the existing cells?

Not at all : you may have as many ENC chart catalogues and raster or Navionics chart folders in the Chart Manager as you need. In MacENC, you may switch, for the same area, between ENC, raster or Navionics in the View menu.

Can I leave these two cells in the Chart Manager with the Navionics cells?

ENC cells are in ENC_ROOT catalogue, Navionics region has his own folder, both in Chart Manager.
About your last question, I did notice a lower speed for launch ENC cells since last release. Wait for the gpsnavx answer...