If I understand your question, then just use the same input name for the output name. The input image will then be replaced with the output in your file system.
convert dragon.gif -fill '#0008' -draw 'rectangle 5,128,114,145' -fill white -annotate +10+141 'Faerie Dragon' dragon.gif
or you can use mogrify to do them all at once. But if they are not all the same size and cannot use the same rectangle and annotate coordinates then this will not work as the command must be exactly the same for all images.
cd to the directory with all your images.
mogrify -format jpg -fill '#0008' -draw 'rectangle 5,128,114,145' -fill white -annotate +10+141 *.jpg
see
http://www.imagemagick.org/Usage/basics/#mogrify
WARNING, be careful as this will overwrite all your images in that directory. It is generally better to create a new directory and use the -path option with mogrify so that you don't lose all your source images if you make a mistake. If no mistakes are made, then you can delete the old directory (and rename the new one to the same name as the old one, if you want).