I drilled my first tank and, IMO, you will want to drill as far down from the top of the glass as you can, but if that is a kit, it probably has a template so you properly place the hole for the bulkhead.
The anti-siphon hole needs to be on your return line from your sump and it needs to be out of the water. Technically you can do without it as long as your sump is large enough to handle the water that will be siphoned back until your return line starts to suck air, but the anti-siphon hole is nice. In my tank, it is just a tiny hole (no more than 1/8 inch) just above the water line in the return line. Note that this will constantly leak water from your return pump such that it won't come out of your return nozzle(s). The idea is that as soon as you lose power or your pump stops, this hole will suck air into the line and break any potential siphon almost immediately.
If your return line will be completely submerged, then you want to drill a tiny hole in the top of it so that the siphon will break as soon as the water gets to that point, but it will probably still run out until the water gets to a certain level. I would recommend putting your return line above water and let it droop into the water so that your anti-siphon hole can be just above the water line.
If you watch this guy on youtube as he plumbs a reef tank, it is very informative as to how you will want to prepare for back siphoned water.
http://www.youtube.com/watch?v=Kn9a1Arvn-YThis particular episode has several parts and it is worth watching because it will help you visualize how plumbing should work.
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