AVR Freaks

God gave you the Arduino MEGA2560.   You can prototype many "2560" projects with this hardware.    There is no need to use any specific language e.g. C, C++, BASCOM, ...

There are Ebay "breakout boards" or an Atmel STK600.

You can develop your project on the proven hardware.

When fully debugged,  you can copy their schematics, pcb layout, ... to suit your final device.

Don't be proud.    If a pcb design is public,  COPY it,

Yes,  it is wise to provide a header for ISP or JTAG an the pcb.

If the design has a USB-Serial chip,  you can use a bootloader (like Arduino).    But you still need one-off access to ISP/JTAG to install the bootloader in the first place.

David.

p.s.   you can develop any "hardware test" program on the Arduino.   e.g. blink LEDs on each GPIO pin.

You can develop more sophisticated sketches and use your Rigol to observe the waveforms.

When your "diagnostics" are proven on the Arduino,  you can run them on your custom pcb.

No, the bootloader does nothing for the running application.
Yes, if you use an external programmer, you will probably erase the bootloader.
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When you have installed a bootloader, BURY the programmer in a deep hole. Always use the bootloader.
If you want to use JTAG or debugWIRE for debugging, dig up the programmer when you want to re-install the bootloader.
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A simpliified explanation. You could put useful code into the bootloader e.g. like a BIOS. But most bootloaders are just small and single purpose.
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David.

OH man, 21 posts into a dead PCB Thread and we are missing the most important information needed:

Please post a true, accurate, full schematic of your project (PCB), including all of the micro's pins, by-pass caps, etc.

Please post a decent photo or two of your PCB.

Maybe it is truly a dead board, and not salvageable, but perhaps there is just an simple correction or two that will bring it to life.

It would be nice to bring this board to life as you might well then learn even some more items you wish to include on your Version #2 PCB.

As for debugging with your scope, some good suggestions were made above.

Hook the O'scope probe's Ground lead up to the Ground on the PCB, or the Ground on the power supply.

Attach a piece of fine gauge wire to the O'scope's probe, it will be easier to use than the probe itself when checking pins on the micro.

Pull out your data sheet for the micro.

Check the power supply's voltage at the input and output of the power supply, if it is on the PCB.

Otherwise check the V+ rail on your PCB.

Check the voltage on EACH Vcc and AVcc pin on the micro.

Try looking at the Xtal pins, one at a time, with respect to ground.

The O'scope can load the oscillator down, and it can stop oscillating, but in the x10 position you can probably see the clock (oscillator) signal.

It will likely be a 16 MHz, roughly sine wave of a rather low amplitude.

Depending upon the O'scope, the uC, the pin you are looking at, and the probe, the clock signal might look somewhat square-ish.

A squarish-ish or sine wave at 16 MHz is what you want to see, not a flat line.

The reset\ pin should be high, (Approx Vcc).

You might well have the ISP header backwards, (as was mentioned above), or have a shorted connection when you soldered on your ISP header jumper wires.

Don't toss the PCB until you have posted the schematic and the photo (s) !

JC

Edit:Typo