You just hold 2 strands together as if they were one. You can keep each skein of yarn in separate ziplock baggies if you want. The yarns will twist around each other when you make the stitch, but you really can't prevent that and it won't be that noticeable after you're done.
As far as working both sides of the border at the same time, there should be instructions in the pattern for how to do it. It may not make sense reading it and trying to visualize what's happening, but could after you get there and have the needles and yarn ready to do it.
sue- knitting heretic