Since this is one of the most important steps in building a guitar, it makes sense to take your time here.
First, I wouldn't drill anything until you have all of the parts in hand.
Stewmac's calculator is really nice and all, but it only works if you're using exactly the same bridge as they're calculating for. You have to drill your holes according to what you actually have.
In my case, I used a vintage scale fretboard and a non-compensated wraparound bridge. I set the bridge so that the ridge for the High E was exactly at the intonation point, with a couple of millimeters of forward action, just in case.
Importantly, I used a pair of laser guides to position the bridge relative to the nut --that is, the outer slots for the E strings.
The result is a guitar that is surprisingly intonated (given the lack of possibility for compensation other than the forward/backward motion of the two sides of the bridge).
A wraparound tailpiece is usually set straight. A TOM-style bridge section is normally set at an angle, with the bass side set backward.
spot on.