If I just want to write my firmware into the ATSAM4L MCU the easiest, simplest way possible, is it really the Atmel ICE using JTAG? JTAG is such a large connector. The AVR MCUs use the ISP port that are 6-pin, so small, and it works just fine.
Also, my board already has an Altera FPGA that's programmed via JTAG. Can I place both the Atmel SAM4L MCU and the Altera MAX 10 FPGA in the same FPGA chain, sharing the same JTAG connector?