Throwing in my two cents worth: Photomatrix is fine, but IMHO NIK far surpasses using control points to finely tune any and all points of the image that you choose. Unless you are very careful and know what you are doing, Photomatrix tends to make the yellows stand out, slightly overwhelming the eye with yellow.
The ghosting is what causes that awful white haloing in skies. With NIK HDR Efx Pro, I found it easy to reduce the ghosting to nil, simply by choosing the lowest number. I do use both programs and many cameras, as well as Photoshop CS6 Extended.
There is no 'right' or 'wrong' way to do HDR. It is all in the eye of the artist, or what you previsualize as your finished image.
I have not found a single camera that produces HDR that is anything but ho-hum. The high end Nikons give you a 2 to 9 bracket right on top of the camera. If you are using a tripod and are very careful, you can start off with a 9 bracket starting at -0-, and I do not recommend doing full stops at using a nine bracket. That will produce almost all white at one end, and all black at the other end. Start practicing with 9 bracket 1/3 stop, balanced at zero. Then learn to shoot for your taste. I prefer deeper, darker images for the most part, so my bracket will often start at -1.3 as the zero point, depending on the subject.
IMHO the ideal HDR does not scream HDR at the viewer...instead, it allows the photographer to bring into view tones and variations that are missed even by the human eye. The tones are there when you shoot, you just don't see them. Furthermore, having all the tones at your fingertips, you can then lighten and darken to suit either using NIK, or NIK Viveza, or even just the burning and dodging tools in your software, be it Photoshop or Gimp or whatever. Instead of making those dodged spots gray, you will actually be lightening true colors and tones.
Last but not least; about layers. Layers for the HDR shooter are wonderful. I have noticed many fine amateur photographers take beautiful images, compile an HDR finished product...and never bother to either brush the effect out of blown-out windows or mask the windows so that just the darkest of the frames has the windows showing (cut, paste to a top layer). That is when it reeks HDR and PP. The very best HDR, IMHO, makes the viewer wonder if it is...or if it isn't...HDR.
Don't be afraid to experiment. It isn't as if you are paying for film or paper. You are learning what you love, enjoy the journey.