Using the following schematic, will I be able to program the arduino? I have a weird feeling that it won't. I've used the same schematic (minus the programming interface) and it does work just fine... I just need to ensure I can program it.
I have a single layer board just about finished, I just cannot connect the second ground connection... I refuse to use jumpers 
Where's the schematic?
Hmmm... I must have arrived in the past before the schematic was there
As far as I can tell, what you posted should work. Maybe I am missing something, but where is the second ground you can't connect?
Pins 5 and 6 on the Program header. A view of the board is below (for real this time ;)):
Pin 6 is at the top of the vertical header.
Is the only point of PIN 6 to add the ability for a filtering cap? If so, then the filtering cap would probably be useless if it is traveling back through a long ground before it makes it back to the board. Also if that is the case, you probably don't need it. I don't see why it wouldn't work without it. I'm not saying that the filtering caps aren't necessary, just that I tend not to use them when prototyping and never have had a problem. Plus in your design it would only be used when the programming interface is connected.
Would I be better of without a ground plane? Or perhaps isolate a few sections?
Personally I would say the ground plane isn't necessary for normal use. But that all depends on your design requirements and the environment that this will be used in.
Hobbiest purposes for this one... I'll scrap the plane and see if I can route things a little better...
Since the header goes to the tx/rx pins, can I assume I would use a serial cable to program it?
Yes... but not serial directly from a computer serial port. You need TTL level voltages. If you are using a USB->serial adapter you are probably ok, but otherwise you'll need to convert RS232 to TTL with a MAX232 or something similar. But it sounds like you might know that already.
1. The Reset pin should be pulled up. Usually it's a 10K resistor to Vcc
2. For auto-reset, with a 10K pullup on the Reset pin, coupling to serial port DTR is usually through a 100 nF (0.1 uF) cap. 22 pF seems a little light. (The reset pulse will be too short, I'm thinking.)
Regards,
Dave
The reset is being pulled up with a 10k... On the previous schematic, for some reason eagle decided to use a capacitor symbol for the reset line (the board had the correct resistor, however the schematic didn't) I've fixed it and it is posted below:
Oh, and I should add that I have used the exact schematic (just without the programming header and support parts) and it works beautifully! 
I just want to make sure that I will be able to program (with whatever cable) the chip while on the breadboard, and if the dual grounds on the cable are required, since I am having one heck of time routing pin six on the program header without using jumper wires (yuck!)
Just looking at the PCB design,
The VCC track from the header to the 328 VCC pin is a bit light for my money. I guess you have to go between pins and it has to be narrow at that point but you could thicken it for the rest of the run.
The decoupling cap is (electrically) miles away from the VCC and GND pins on the processor, it should be as close as possible and could easily fit between the reset switch and the crystal (if you move one or both a bit)
I am having one heck of time routing pin six on the program header
I don't get this, isn't it routed to GND already?
I will likely redo the whole board later today...
Pin 6 is connected to the ground plane, however the segment it is on does not connect to the rest of the ground plane due to traces. I'll post back with my progress.
Does the connection of the program header make sense though? Will it work?
however the segment it is on does not connect to the rest of the ground plane due to traces
Oh yes I see. When you move the decoupling cap down near the power pins on the uC you won't have the trace between pin 5 and 6 on the program header. If you don't move the cap you can run its trace directly to the left most pin on the IO header.
Will it work?
I think so (with a larger cap as already mentioned), I'm designing the same circuit into a board at present so we're either both right or both wrong
But what is the header connected to? Is this 6-pin SIL header a standard or are you wiring up a custom cable?
Not too sure about the cable. I assume I'd need to wire a custom cable, but that shouldn't be an issue. A standard serial cable with an off the shelf serial->usb should work. Right?
I've redone the routing a little bit, changed out the 22pf to a 100nf, moved the filtering cap (I blame the rats nest during layout, it was connected to the program header, my Connect Fourduino prototype v3 has the cap within 3mm of the atmega).
Yeah, there's a jumper and I HATE it! However it IS under the chip so I won't have to stare at it all the time
Have a look at the FTDI cables, one of them has a SIL-6 connector that would suit very well I think (different pinout though :()
I don't have a link right now but the document that describes all the cables is DS_TTL-232R_CABLES_V201.pdf, which I think I got from the FTDI web site. (I notice that the SF page has a link to FTDI_CABLE_V205.pdf, maybe that's the same doc)
You could get rid of the jumper by running the pin22 GND out through the header strip. Keep it thick but neck down briefly when going through the header.
There's a couple of unnecessary corners in traces but it's looking pretty good.
Rob
Woot! I cannot believe I didn't see that route myself.. lol I went ahead and beefed up the rest of the power and ground traces. I think I'm done now I've been itching to do some more etching and I think the time has come!
itching to do some etching
You can say that with a straight face?
