In my experience, Fix-a-flat is a permanent, but unrepairable, fix. In other words, you can use it for a small puncture, but if it doesn’t work, you’re boned. The tire cannot be patched later.
The unbalancing problem is very real. I, too, had a nail stuck in my tire (through the thickest part of the tread!), giving it a slow leak.
I sprayed in fix-a-flat, but it didn’t work (though it has worked OK on other tires). In fact, it never fully solidified, and the goo would randomly spin about the inside of the tire, making for a hell of a bumpy ride and a tire that was impossible to balance. I had to get the tire replaced.
My advice: drive the car, with nail still in the tread, to a trustworthy repair shop (Sears does a good patch, even) and have them remove it and patch your tire. I don’t think I’d use fix-a-flat again, unless it was a serious emergency (i.e., truly life-threatening, and I couldn’t spare the time to change the tire and then get the tire patched).