In-System Source and Probes Usage

You can use it for any purpose that fits your application. I've used it (together with In-System Memory Editor) for calibration and test. Unfortunately, there's no documented API in the Altera JTAG stack for Source&Probe and other virtual JTAG functions. So Source&Probe capabilities practically depend on the effort your willing to spend to understand the interface.

The topic, also possible interface to user applications has been discussed in the forum before.

Another usual method to program memory connected to JTAG capable devices is by generic boundary scan access to the CPLD/FPGA pins, although it's rather slow.