Power/voltage management with 6v battery

I'm retrofitting a device and one of my constraints is that it it powered by a 6v 1.4aH SLA battery. I also need to be able charge this battery.
My first thought was to get a 5v buck converter, and splice into the USB power supply so that the battery supplied 5v through the USB port.
I've got to use USB to read a stream of data from a digital scale and also allow the downloading of collected data (but not at the same time). The USB scale is not powered via USB.

The device is waterproof and I've got two bulkheads available to me. My first thought was to use one bulkhead for USB communications, and the second for charging the battery with an external 3 stage charger. The arduino would monitor the current or voltage on the charging bulkhead to know what mode the USB connection should be in.

My question is, can I just attach regulated 5v into the USB red wire and still be able to plug into my computer or an external device? Is backfeeding 5v an issue?

I'm not sure which Arduino I'll be using, but it will either be a Mega2560, Due, or ADK. The 5v bus is not important for what I'm doing, but I do need the 6v to power some hall sensors. I know the minimum suggested voltage for Vin is 7v, but will the Due, being a 3.3v design, be unstable if I power it with unregulated 6v through Vin? I don't need regulated 5v for my application.