In Quartus II, launch the Programmer and set the Programmer options to enable real-time ISP. Once this option is set any action issued to MAX II in the programmer will be issued using real-time ISP.
To change Programmer options:
1. Choose Options (Tools menu).
2. In the Category list, select Programmer.
3. To allow background programming in devices that support real-time ISP, check the Enable real-time ISP to allow background programming Option.
4. Click OK.
For Jam or JBC you must use a -d option in the command line to enable real-time ISP for the actions issued in that same command line. There is a -d option called DO_REAL_TIME_ISP. Set this to =1 in command line to enable real-time ISP. An example is shown below:
jam -aprogram -dDO_REAL_TIME_ISP=1 <jam_filename>