Hogan is right. The video file will be the same no matter how you deliver it to your favorite third party editor.
The point I was trying to make a couple of posts back is that the file handling software that comes with your camera will do some basic editing but also does some extra "features".
I was not clear about "features". For example, the Sony PMB software can link your videos (or photos) to a google map so you can see where you took them. The camera needs to have a GPS, like in the HX9V, and the position data needs to be recorded somewhere -- like in the .modd or .moff files. Another example is the ability to use PMB to put files back on the camera so that (with the right cord) you can play it on Grandma's TV at Thanksgiving.
My Panasonic camcorder makes four extra files for each video. They end in .tmb, .pmpd, .moff and .cont. I don't know what each is for, but without them HD Writer (the Panasonic version of PMB) won't do anything.
To Hogan: PMB allows you to be very neat and tidy with your clips if you let it keep the extra files. It gives you a choice of neat and tidy file views or calendar views. The easy trimming and joining of clips in original quality seem to be unique to the camera provided software, like PMB. Apparently the third party editors have to deal with all the brands and formats so they can be a year or two behind on certain features. And, they have to be far more complicated because, to be competitive, they have to include an amazing list of functions.
To Hillarythehorse: PMB will transfer videos to you computer from either your camera or SD card. It will put them in a folder of your choice and include the extra files. The convenience level is as good, or maybe better than Windows Explorer.
To Both: Once you move your original video files with PMB, leave them where PMB put them. If you want to rename or move the original, use PMB to do it. You can use Windows, DOS, backup software or anything you want to copy those files for any use you have. All digital editing software, including PMB is called "NLE", or Non Linear Editing. It is a big deal because tape systems couldn't do it. It means that the original is never moved, modified or renamed. It is only referred to and used to make new files.
When I first got my Panasonic last winter, I ignored the software, copied with Windows and then cleaned up the SD card with a format. It seemed neat and tidy. Then, when I wanted to join a couple of clips, the software wouldn't let me because I didn't keep the extra files. I haven't tried that exercise with PMB, but I'm pretty sure it would be the same. Hogan, you could a few short clips of the dog, kid or something, copy to your computer, delete the extra files and then try to join them in PMB. If it works, let us know.