Neat tool.
When interfacing with existing hardware with DTR reset circuit, all you need to do is close and reopen the serial connection - also, there is probably a way to manually twiddle the DTR pin (see the documentation for the serial library in whatever language you're writing that in).
On the hardware side, the DTR pin is connected to one side of a 0.1uf ceramic capacitor. The other side of that 0.1uf ceramic capacitor is connected to the RST pin on the AVR, and pulled up with a 10k resistor to Vcc.
Thus, when DTR goes low and stays low, the RST pin initially goes low, but is then quickly pulled back up by the resistor. When DTR goes high again, that's okay, because the RST pin is rated for up to 12v.
Some people put a diode from RST to Vcc (with the band towards Vcc) to prevent reset from rising above Vcc - on the unproven theory that some otherwise unexplained brickings were caused by briefly entering HVSP mode).