1. I'm a bit confused, I keep seeing people using Vcc to power stuff, is it an input, output or both?
It's both. If you put battery power to the RAW pin then you are supplying power to the Arduino's on-board voltage regulator, which then regulates the voltage to the 3.3V rail on the Arduino itself (in the case of a 3.3V pro mini, it's 5V for a Nano or 5V pro mini).
The VCC pin on the Arduino is tied directly to the Arduino's 3.3V rail, so if you have a regulated supply at the right voltage then you can go right to that pin. By putting power to the VCC pin you are bypassing the voltage regulator on the Arduino board.
Now here's where it gets tricky. If you put power to the RAW pin, that will cause the voltage to be regulated to 3.3V (or 5V, depending on the flavor of Arduino). That VCC pin is still tied directly to the Arduino's regulated power rail, so it now becomes a source of regulated voltage!
So, if you power the arduino with regulated voltage, the VCC pin is an input. If you power the Arduino with the RAW pin, the VCC pin is an output. Neat, huh?
2. Through hole vias may be too big for this to work and if I did use them, they would probably be very small anyway but I will look into it.
Spacing the pads out any further will make them hard to bridge so I might just pre bridge them and have the end user tell me which setup they want to go with when ordering.
That sounds like an excellent idea.
3. When I talk about the WT voltage I do mean it's main power, mem voltage stays at 3v3.
Ok, I was just noticing on the diagrams that you posted that the 3.3v pin on the WT588D had nothing attached to it.