How to Make a Good PCB - Design Problem

Hi, all
This is my first attempt at doing this. I want to try my hand at creating a consolidate PCB. Also I am using Eagle for this, again a first time user.
My Goal: a single compact PCB with the Atmega32u4 & BNO080 connected together via I2C, an ICSP header for programming the 32u4, a buzzer as the output, and two 2032 coin cells to drive it. This will be a 3.3V board.
Would someone be willing to review my schematic for errors/omissions?
Schematic source:
Atmega32u4 datasheet:

My ex company used to populate circuit boards for University Engineering students. The top problem they had was matching the components foot print size from the bill of material to the pad size on their circuit board. Something for you to watch for.

I can give you a couple of pointers:

  1. If you have not yet learned Eagle you might look at Kicad. It is open source and seems to have a clear future at being free.

  2. Before you sent your board off for mfg, print out a 1:1 and physically lay the components on the printout to verify the right connections. This is not just for a first timer but anyone who has not already physically verified the library footprint.

  3. The crystals and their associated capacitors need to be right at the ┬ÁP pins. No meandering traces.

  4. For a 1st time design I would recommend you do not connect traces under the parts. It is inevitable that you will find an issue and have to cut and jumper some traces.

  5. I would not use the mfg minimum spacing and trace width. This is a limit not a recommendation.

Thank you for helping...

I found that battery selection has been a challenge. I spent two days last week scouring the internets learning about batteries for projects like this. I have little space and specifically want a replaceable battery (versus lipo recharging). I considered a 9V box battery, but lots of comments regarding their inefficiency, especially when used with a linear regulator and 3.3V needs. Opinion on this? I don't need really long life. 200 mAh battery would be fine, and I believe even a poor 9v would provide twice that.

I tried to run my bread-boarded prototype with a single 2032, but it would not run... hence ending up with two in series.

Is this due to the fact that the single 2032 battery was being run through the Pro Micro regulator along with running the on-board LED's? I can try removing the regulator and led's from one of my arduino's to see if it will run with a single 2032.

A single 2032 provides about 3V which is not enough to power the Pro Micro when applied to it via the voltage regulator. When you tried a single cell where did you connect it to on the board and similarly for 2 in series