Hello - I am a relatively new user too, but after running the NEEK for a month it quickly all fell into place -
1. JTAG yes.
2. The C3 will configure from Flash-ROM automatically on power-up - there are several other options such as serial configurators, it's all pretty much well described on the altera website - The hard part is not getting your device configured, but protecting your design.
3. SOPC builder integrates NIOS II and everything required such as DDR Bus controllers into one package, it is part of Quartus and is freely available from
altera.com I'd suggest playing around with a NEEK if you can get your hands on one, it will provide you with a platform to base your design around.
Hope this helps.