For simple edits I just flatten and save as a .jpg (but I don't overwrite the original file).
For more complex edits (typically anything with layer masks or more than a few layers) I save as a .psd without any merging or flattening, then I do resizing (and output sharpening if necessary) and save as .jpg (sometimes I flatten, sometimes I don't bother - doesn't seem to make a difference). I don't resave as a .psd when closing the file (so the resizing is not stored in the .psd).
If I have a situation where I have layers that I haven't used in the final output (some experimentation for example) I sometimes do a 'stamp visible' prior to saving the .psd file to give me a reference point of what layers I had used when saving the .jpg file.
I was doing this but found that the EXIF data wasn't being transferred to the new document. Could have been a setting somewhere perhaps, I didn't bother chasing it up.
Cheers.