It really depends on what you want. For me the two front runners for Organising, tethered capture and post capture processing would be Lightroom and Capture 1.
I use both and find that Capture 1 better for Tethered capture whilst Lightroom's tone mapping seems to be more intuitive, but they are both excellent processing tools for Raw conversion, but that's just my opinion. We all have our own way of doing things

Hi
You have had several responses to this post so I'm not sure if this will be of any use but here goes
All edits to your images are none destructive so your original files are ok, the changes you make are stored in sidecar files (XMP file extension) alongside your original raw files in the same folder so this is the first thing to check. If your sidecar files are here you should be able to recover your work
The Catalogue is as previously mentioned a data base that knows where all your files(original and sidecar) are stored. I personally opt to back this up every time I exit Lightroom (go to Catalogue Settings on the Edit drop down menu).
I wouldn't dream of telling you how to organise your workflow but I always import direct to Lightroom, that way Lightroom always knows where my images are, and what changes I have made

If you haven't already seen it I would recomend watching a YouTube video by Tim Grey called getting organised in Lightroom. He also has many other excellent YouTube videos on organising and editing in both Lightroom and Photoshop
Best of luck

Lightroom 6 to expand on my previous
By adjusting the shadows and highlights sliders and setting the black and white points using the black and white sliders in the Basics tab of the develop module you are tone mapping you image, whether it be a single image or an HDR image generated from bracketed images via photomerge. For me this produces a more natural looking image, more like what I observed and wanted to capture. I find that Photomatix tends to give more graphic style images
It is of course all very subjective and down to personal choice. As I said before, it works for me

To my mind you have all you need with LR6 but to increase your options the NIK collection is a really good free plugin. In LR6 you can 'photomerge' several images to produce either panaramas or HDR images. Once merged you have the full power of LR6 to tone map and tune the image to suit . I only use LR6 with the occasional adjustment in Elements. It works for me!