Ok, thanks, I'll replace the pads with the same technique of inserting an svg image as a logo object and putting into the copper layer. Will these still be the same thickness and work as well with capacitive touch (MPR121)?
With the holes, It's basically that they are not visualised in this 3D gerber viewer : http://mayhewlabs.com/webGerber ... but when you load one of their example boards you can see through all the vias and holes. Perhaps Fritzing outputs a different Gerber file name convention that Eagle?