so the level shifter is only needed if i power it all off the single large PSU?
Some have problems with flickering and other led strangeness without a level shifter, some don't. That being said, the led is looking for a 5v data signal (+/- about 5%). And the Rpi's data pins are 3.3v. Some led's have a wider tolerance of the data signal and handle the lower voltage data signal better.
does it matter which GPIO pins i connect too?
Oh,and in that first diagram, think of the battery packs as your wall wart and . .err . .Big Bertha power supply.
I'm making the assumption that your using a led strip that has a clock and data connection. If its a one pin led data strip, then omit the clock line.
Hope it helps.
P.S. good tips and stuff on this page https://hyperion-project.org/t…-ws2801-ws2812b-apa102.8/