First, a decoupling capacitor isn't needed on the DS3231 Vbat supply unless it is the only power source, Ie Vcc not connected. If it is just used for battery backup then there is no need for it. In fact having a decoupling capacitor there will drain the lithium backup battery faster.
I was looking at that long +5VDC trace. If you swapped the battery and clock with the logic level converter and atmel, and rotated the logic level converter 90 degrees, the length of the +5VDC trace would be roughly halved. Also the heavy 3.3VDC user, Atmel, would be closer to the power supply.. The clock chip uses so little power it just needs a bypass capacitor for it to be happy with it's power supply trace. I routinely power them using 5+ inch long 30 AWG VCC and GND wires with no reliability issues. The I2C carrying traces going to the Atmel can be long if needed. Just keep them the same length. On the other hand the +5VDC trace powering the logic level converter gets a workout when the LEDs are being updated.
If you need the time to be maintained for more than a couple days, feel free to ignore this. Another change I would make is swapping in a 0.47 Farad super capacitor in place of the lithium battery. A 3.3V or higher voltage super capacitor can be charged from the 3.3VDC supply using a diode, and resistor in series. The diode should have a very low forward voltage drop, and low reverse leakage current. Diodes with a reverse leakage current of 10 micro amps or less do very nicely. Search first for low forward voltage drop, then sort on increasing leakage current. Leakage currents down into the pico amps are available, but they often have relatively high forward voltage drops and cost much more. Size the resistor to set the maximum initial charge rate when the super capacitor is at 0 Volts with no charge. I use 25 to 50 mA. The charge rate will slowly lower as the super capacitor's voltage increases. It will charge up to 3.3V minus the diode forward voltage drop for < 1 mA current over a few hours. I've been using a diode that only has 0.3V drop at very low mA currents. A 2.95 Volt charge in a 0.47 Farad super capacitor will backup power the DS3231 for 2 to 4 days before it drops below the minimum voltage new temperature correction adjustments will still be calculated. My tests show the oscillator will keep working down to just under 1 Volt which takes a few more days to reach. It just looses adjustments to the temperature adjustments. 2 days should weather most power outages. Yeah, it's not years like a lithium battery, but it can be shipped with no lithium battery restrictions.
The super capacitor I've been using for my clock backup circuits is also able to be reflow soldered. No hand soldering or installing a lithium battery later. The main downside is cost. At $5.60/Q1, $3.32/Q200, the super capacitor is much more expensive than a coin cell lithium battery.
This diode CFSH05-20L from Central Semiconductor Corp is better suited than the one I use. Only 0.16V forward voltage drop at sub 1 mA currents. I may switch to it or another one.
https://www.centralsemi.com/get_document.php?cmp=1&mergetype=pd&mergepath=pd&pdf_id=CFSH05-20L.PDF