That's correct. One copy will be saved on the iTunes library and the other one will keep on its original folder. If you don't tick that option, the song won't be copied to the iTunes library, so it will disappear when you transfer the iTunes library to other PCs, Macs and devices. You should tick this option to simplify the iTunes library migration to another PC or Mac in the future
To avoid the duplication that the option Copy to... might create you can move the files to the iTunes Media folder (iTunes Music was an earlier name for this folder). If you're happy letting iTunes organize the content then move it to iTunes\iTunes Media\Automatically Add to iTunes otherwise if you have turned off the Keep organized....option place it where you want inside the media folder before adding to the library. As above having all the media inside the iTunes Media folder will aid with backups and future migration to a new drive or computer.