Here are step by step instructions on how to copy ATR files from your PC to a real floppy disk. This uses RespeQT, SIO2PC, and Copymate. I just went through this, and it works great!
Write Atari 8-Bit Computer ATR Files from Your PC to a Real Floppy Disk Using the RespeQT Peripheral Emulator Software and an SIO2PC Adapter (15-30 minutes) – Atari Projects