Personally I find the uploaders to SmugMug in Lightroom and ACDSee to be very clunky at best.
The key is organization, that is, good file asset management. Come up with a work flow and directory structure that includes a final place to store your images. From there copy the ones you want to upload to FAA into a folder called "FAA". Simply browse to that folder to upload. Works every time.
Although Lightroom has asset management built in, I don't find it very intuitive. And I'm a Systems Administrator in my day job. I use ADCSee Pro. Very simple and easy to use without a lot of tutorials. You can copy and move from folder to folder and know exactly where you are keeping something.
Bradford, LR doesn't "save" anything in a proprietary format. It's non-destructive editing. The original RAW file never gets touched. Exports are to common formats like .tif and .jpg. If you want to save the edits, simply keep them in the catalog. I find if for some reason I ever need to go back, I generally prefer to reprocess the shot anyway.