Gotta understand RAW
Unfortunatly they don't, when using NX I pull from folders on the hard drive like you say. What I do is I import by date using LR, I'll sort through the images flagging really good shots and deleting any that I don't like, then I close down LR, open NX, select the folder of images that I want to work on and have at it. It's a rather clumsy way to go about it but it ain't bad. LR simply makes it easy to find older shots or shots that I have't processed. I simply have to cross reference the date if I want to open and work on a that particular shot in NX.
There are lots of folks who would like to use Capture NX with other applications; either because the like the fact that it uses in camera settings or because they believe that it does a better job of demosaicing. There is no graceful way to do this beacuse of the nature of RAW files and non-destructive workflows. The full answer is way beyond the scope of a forum post, but perhaps this may be helpful:
-- RAW files are just that, the most basic image data from your camera. (A RAW image is actually just light levels - doesen't even have color.) RAW files can only be written in a camera and cannot be modified. Nor, for that matter, can they be seen. (A bit similar to undeveloped film.)
-- RAW files must be read by a "converter" or, I prefer, a "developer." Originally, all RAW files were run through a converter (often as a batch job) and written as industry standard JPEG, TIFF, or PSD files. These files were then placed in your catalog and edited as you wish. Simple.
-- Then some smart people noted that most of the editing potential lay during the actual "conversion" or "development" process - you had complete control over white balance, you could alter exposure by several stops without damage, etc. (Most RAW files are 12 bits or more.) This was much, much more powerful than anything that could be done later once the RAW was reduced to a compressed 8 bit JPEG or even a 16 bit TIFF. So everyone started doing a lot of "pre-editing" during the "conversion" process.
Capture NX sits at this point. It will read a RAW file (NEF), development, adjust it, and display it. The adjustments however are ONLY visible in Capture NX. They can be "saved" by writing them back into a portion of the NEF, but the RAW portion is never really changed, the image must be reconstructed on the fly every time you see it. You can, off course, convert the NEF into a JPEG, etc.
Aperture and Lightroom go further, by wrapping a database around a RAW engine. That is, they hold all of your images and give you powerful organizing a selecting tools. When you select a RAW image they will develop and display it and allow you to adjust it. Your edits will be saved in a linked file in the database and recombined as needed. As with Capture NX, this process is transparent to you, but, of course, your "edits" cannot be seen in any other program. Again, you can print or convert to JPEG, etc.
The advantages of this non-destructive RAW work flow are:
-- RAW files hold more data than JPEG and are much, much smaller than TIFF or PSD.
-- The database (and the nature of a RAW file) assures that your orignal file is never lost. (Bit like a negative archive.)
The disadvantage, as Trevor noted, is that you cannot mix and match your favorite RAW developer with your favorite editor with your favorite database.
Sorry this is long and complex; hope it helps. I have found that most people who are having real trouble shooting RAW are unsure on one or two of these basics. (And apologies in advance if I was not clear or got something wrong.)
