Most fab places are only going to produce what you send them in a “raw” form (usually a collection of gerber files). The onus is on you to design your “base layout” correctly.
You don’t say whether you have used PCB layout apps before - if you’re a novice that can be somewhat daunting (ask me how I know )
here’s what I would do.
Grab the free non-commercial, limited PCB size version of Eagle - if you’re comfortable with any other software product and have that, then use that too (you may have trouble finding the Arduino header locations in anything other than Eagle though, so you could either measure and layout your own or try converting the eagle file you’ll locate in a step below).
To get the raw layout of the header positions, you could hunt for an Arduino library component (that will work for a Domino, or a Panda if you only want to use the regular pin layout).
OR: Take the design files from the Domino (or Panda), go to schematic view and throw away the unnecessary parts (including the USBizi), leaving just the headers (which are the pieces you really need).
THEN, either way, add your additional parts and wire them together appropriately. Then turn that into a PCB layout.
Personally I’ve designed a custom shield that I want to try to home manufacture using press-n-peel toner transfer and etching. Attached is an early attempt, that has some home-etching design issues that I am working through (lucky that easter break is coming up!). I just took the Panda design file as my starting point, threw away everything, then added my parts including a custom footprint for a full-size SD card holder. Wasn’t overly taxing, and it would work as-is if I sent it to a fab house (I would try out ITeadstudio’s PCB service first) but this is totally a one-off so I can’t justify the additional 9 boards that would get manufactured and never used, which is why I will choose to home-manufacture it.
so… what you want to do and I might even be able to help get you started