Links to all manuals we use:
The first board will use a Cortex-M3
- ARM Cortex-M System Design Kit (pdf)
- ARM Cortex-M3 Devices Generic User Guide (pdf)
- Cortex-M3 Technical Reference Manual (pdf)
The chip we are currently using is an Atmel SAM3
- Atmel Crystal Oscillator and PLL Considerations
- AT03499 - Getting Started With SAM3S Microcontrollers
- Olimex SAM3-H256 Manual and Schematic
- Olimex SAM3-P256 Manual and Schematic
- SAM3S Datasheet
- SAM3S Schematic Check List
- FTDI C232HM
- Take a look at jtag/sam3-C232HM.png to stop worrying about the plugs