Active Serial (EPCS) and JTAG Connection Cyclone IV

I would use the simpler circuit according to device handbook: figure 8–29. programming serial configuration devices in-system using the jtag interface

Unless you have existing programming equipment that isn't prepared for JTAG indirect configuration device programming, you can save the AS programing header. The comment about MSEL in your schematic is at least misleading. Normally, MSEL would be jumpered in your circuit for an AS scheme. JTAG programming can be always performed in any chosen MSEL configuration.