You don't "adjust" output current. Loads draw whatever amount of current they need, provided the power supply can deliver it. If your total load exceeds the buck converter's rating of 3A, then you will be overloading it. If your total load is less than 3A, then you need not adjust anything.
I'm not familiar with your battery, but keep in mind that the input power will be equal, minus efficiency losses, to the output power. For example, if the load requires 1A at 5V, that is 5W, thus the input at 9V would require more than 556 mA.
As the battery is depleted, the voltage drop will cause the buck converter to draw more current, which will hasten depletion. At some point the battery will be unable to provide the voltage needed by the buck converter.
Your battery manufacturer should have a datasheet that shows the battery performance characteristics, and from that you should be able to ascertain whether it can support the device and for how long.
Per the BeagleBoard-xM System Reference Manual, the current drawn by the BeagleBoard-xM is 350mA to 750mA at 5V (depending on whether it is powered over USB or not). However (page 136 of 164) it is recommended that a 1.5A or greater power supply be used:
It is recommended that a supply higher than 1.5A be used if higher current peripherals are expected to be used or if expansion boards are added. The onboard USB hub and Ethernet do consume additional power and if you plan to load the USB Host ports, more power will be required.
I would recommend measuring your current draw while using a bench power supply, and then determine if the battery can support it. The xM is designed to provide power to peripherals, so you have to take into account whether you or some end-user is going to plug in a USB device or something else that would exceed your power source's capabilities.