Powering board and charging coin cell at the same time
This fellow created a USB charger for those. If you are working with a custom board, you can integrate his schematic into yours:

http://chasingtrons.com/main/2012/3/26/cr2450-coin-cell-charger.html

From the MCP73832 datasheet:
Check out the "typical application"







simulate this circuit &ndash; Schematic created using CircuitLab

This delivers 5V to LOAD when powered by USB; if LOAD is an Arduino, that not a problem. This is compatible with chargers that go Hi-Z when finished charging. The Schottky will protect the battery from the 5V and minimize loss while the device runs off the battery. The other diode is less critical, but might as well be Schottky too.