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I'm talking about the 3 boxes that form a column, near where it says 5V on the top of a lead and 3V below it. The lead comes out of the middle box.
The datasheet for the AT90USB1286 mentions nothing about this, only that there should be 22Ohm resists between D- and D+ (check) and a 1uF cap to UCAP (check).
USB1 supplies 5V (default usb power).
It is a jumper with 2 options. It can be implemented as SMD pads or a pin header. Only one option should be populated.
By default the Teensy 2.0++ (along with the rest of the Teensy line) uses the micro-USB port for power (5V DC). The boxes on the schematic refer to pads on the bottom of the board that can be used to select between three power options:
5V power from USB (default)
Two of the pads are connected by a small trace.
Battery power
Battery power (as low as 2.6V for the 2.0++) can be fed via the VCC and GND pins. To do this the trace between the pads must be cut:
Source: PJRC.com -- The image above shows a different Teensy board but the 2.0++ is similar
This page goes into more detail including adding diodes to switch automatically between USB and battery power.
3.3V operation
The Teensy 2.0++ can also be modified to run at 3.3V. To do so, a 3.3V voltage regulator (such as the MCP1825S-3302E/DB) must be soldered to the three pads under the USB jack. The trace must be cut and the center and formerly-unconnected (3V) pads bridged with a blob of solder:
Source: PJRC.com -- The image above shows a different Teensy board but the 2.0++ is similar
This page goes into more detail on this option.
