Atmel ICE and other stuff

You guys have been most helpful. I'm still making lots of syntax errors, but I'm getting pretty good at finding them. My sketch is getting pretty complicated so I purchased an Atmel ICE for use with Studio 7.

A new regulated 5 VDC power supply just arrived and I'm about to hook things up, but I have two questions..

First, how is the 6 pin connector plugged into the Mega 2560 board? I found one photo of the connector with VCC and GND indicated and it appears that the indexing tab on the connector should face away from the reset button. I haven't found any official information on this so I'm a bit nervous. I bought a second Mega 2560 board just in case.

Second, there are some comments on the internet that suggests that improperly ending a debug session with the Atmel ICE unit can reset some fuses rendering the MCU inoperative. I don't intend to change any fuse settings, but it a concern that I could unintentionally brick the processor. Does anyone have any insight into this possibility?

Re: orientation of 6-pin ICSP connector on mega2560 - just check it with a multimeter. Better safe than sorry (though I've plugged in USB asps into headers on my ATTiny's the wrong way around all the time, and it's not killed anything yet)

MISO 1 2 VCC
SCK 3 4 MOSI
Reset 5 6 Gnd

Pin 1 is usually pretty clearly marked.
If ICE is setup like AVR ISP MKii, it only monitors VCC, and will not power the board.

I often see RST marked, not MISO