If you want to use the pulse entry method using DTR and RTS, which is the most reliable way to enter ISP mode (as it doesn't rely on any user code), then you need to keep changing the jumper.
If you want to use a software-based method such as break detect, Erik's notouch or something else, then you leave the jumper in the Run position all the time.
You could always modify the circuit to replace the jumper with a transistor and use a spare wire in the RS232 cable, bringing it out to a switch at the PC end, if you want a remote method of selecting the mode.
