The Altera Cyclone Programming device EPCS1 are shown to be programmed in the AS mode requiring an own connector. Since the JTAG was never officially declared outdated, I'd expect a way to program the cyclone plus the EPCS1 in JTAG mode. I wasn't able to find it yet though.
Rene, The Cyclone FPGA can be configured by JTAG 1149.1. This can be done through the various download cables, or from a microprocessor. The microprocessor can do this via Jam (also used for programming CPLDs) or JRunner (a simpler FPGA-only tool). For more details, please consult Chapter 13 of the Cyclone Handbook: Configuring Cyclone FPGAs.
The EPCS Serial Configuration Devices are programmed through a serial interface. While the device itself does not include JTAG, we have developed a method of programming it by JTAG by routing the data through the Cyclone device. In short:
The Cyclone FPGA is configured through JTAG.
The EPCS programming data is sent from the PC to the JTAG port of the Cyclone FPGA. This is done by Jam, so it can come from a PC, or from a Jam player running on an embedded microprocessor.
The logic in the FPGA captures data from the JTAG port of the Cyclone FPGA, reformats it to conform to the EPCS interface, and drives it to the EPCS device.
This capability (as a reference design with documentation) is available in beta form today, and will be included in a future version of Quartus II software. To get access to the beta version, please contact your FAE or Regional Support Center.
So, while the EPCS device is not directly connected to the JTAG chain, the device can be programmed by a JTAG controller by passing the data through the FPGA.
One final note - Altera also provides a tool called SRunner, which enables you to program the EPCS device directly from an embedded microprocessor. This is another solution to the question of how to program the EPCS device.
Cyclone FPGAs are programmed using JTAG, or by Altera configuration prom devices, or by serial interface from a microprocessor or download cable. The EPCS1 configuration prom device is programmed using AS protocol, and does not support JTAG.