Design Rules(Eagle DRU File: http://content.laen.org/pcb/LaenPCBOrder.dru) The minimums are: 6 mil trace width 6 mil spacing 15 mil clearances from traces to the edge of the board 13 mil minimum drill size. 7 mil minimum annular ring
Screw it, I'm waiting for a 7GiB download to finish. Look over the attached PDF. If it's correct, I'll export the gerber files.
Do me a favor, and check the traces. I actually have not done any of the rule checks or anything like that yet. If it's all the same and I didn't forget or miss anything, I'll go through the rule checks and all of that.
If you draw the schematic first, it makes creating the board much easier. But if you just can't figure it out, I'm willing to help.
Can you high light the traces that are carrying VCC? I like to make those traces thicker. Also, which ones are meant as ground?
Then those VCC lines need to be interconnected ... You have different, separate traces for VCC. Unless they are different voltages, they need to be interconnected.
You're saying the two bottommost pins are 9V raw input? Yet, it's the same color as your 5V line? Do you understand where or why it's confusing?
So if I understand you right, you have 9V (Vin) being supplied on the bottom. The 'T' shape traces are +9V, correct? From there, you have two regulators, one that regulates down to 3V3 (V3V3) and one that regulates to 5V (V5), correct?
Then, V3V3 is a single trace that goes up to the logic level as well as the HH10D and the BMP085.The V5 trace goes to the DS1307, runs on the right hand side up to the logic level and on the way also connect to two additional pins around the Mini.
Question: what's the red bridge across the two pins on the left hand header? If that's supplied voltage, where is that coming from? It's not connected to anything.
Same thing on the small board, if it's being stacked ontop of the larger one, where is the V3v3 and GND being supplied from? Which pins are they being connected to?
Understand that I'm not trying to be a pain here. I want you to get a board that works, not one that once you connect stuff to it you realize something's amiss. Not knowing what the electrical diagram looks like, I have to rely on you to explain these bits and pieces.
You could take advantage of ground planes also, will give you more room for your thicker traces.