Arduino and Backup Battery Power
If you look at the Arduino Uno v3 schematic, you'll see that the onboard jack has a series diode between it and VIN.  If you've got a series diode between your battery backup and VIN, then you are replicating the dual-diode configuration that you're already using...you'd just be leveraging one of the diodes on the Arduino PCA. 



Note that this doesn't address charging of your battery, but it doesn't sound like that's addressed in your current arrangement, either.