Much research online has revealed that apparently the Trinket doesn't show up when programming it over USB. The Raspberry Pi hasn't been much help yet, but I think I have figured out a solution using the GPIO on the Pi to just code the Trinket over SPI, but I haven't tried it yet.

I have worked on getting the LiPo backpack configured the way I wanted to, because originally it was just soldered on to test. Here I you can see that I have desoldered the backpack and bent it around to access the underside of the board. I covered the .5A jumper with electrical tape and soldered wires to the power switch pads:

Here's the top view of the same thing:

After being bent back into place and resoldered, I cut the trace between the pads for the power switch so the power switch would actually work. Otherwise it's on the entire time the battery is connected and it has a charge in it (kinda annoying, but I see why this is the default). This pic is close enough that you can see the razor cut between the pads. I didn't think it was good enough first try, but a quick continuity check with the multimeter reassured me:

Finally I had to verify that the switch wires weren't going to contact the Trinket and mess anything up in operation:

I'm done with this for today. I may do some more work on the code upload situation later tonight, but either way I should have that part figured out in the next couple days at least.