the only problem you could potentially have with more landscape fabric is it getting clogged up with silt, etc and then slowing down water flow. however, if this is happening, it would have worked its way down over time and clogged up the fabric around the drain line instead.
so, my perspective is this. lay fabric in the bottom of the trench, with enough left hanging out to lap back over the top when the drain is finished, creating a fabric shield all the way around the gravel. if you have problems with clogging up the fabric, its at least better to have it on the top fabric that is easiest to get to and replace, than on the fabric wrapping the drain pipe. clean fabric won't cause any significant problems, unless maybe you decide to put 20 layers down or something.
and yes, holes should always be down. there are some custom applications where you could do a holes up setup, but its not a french drain. it would be integrated into a waterproofing system where all water must be drained away. a french drain should allow water to percolate into the ground naturally, and simply carry away the excess that can't soak in quickly.