Others will probably have a better solution, but here is what works for me.
I tried .dng and promptly abandoned it as it doubled my workload. And made me want to blow my brains out. You can always archive a copy of the dng converter if you are worried about you camera's files not being supported in the distant future..
I manage my workflow from LR and never use Bridge. All images are opened into Photoshop from LR, and so when I hit Cntrl S I know LR will just update the image and no new file is being created..
My folder structure goes: year/shootdate with some basic details. In each shootdate I have usually 3 sub-folders: Raw, Edits and Print. So if I open a file into Photoshop from the Edits folder in LR and want to place a softproofed copy in the Print folder, I duplicate the image, close the original, then flatten the layers and use “save as” and then hit “synchronise” in LR.
If I want to do more work in LR on a file that has come from Photoshop, I create a new sub-folder and label it accordingly. Otherwise I just start drowning.
Archive the entire folder and you should never have a problem with sidecars going astray.
Good luck, David