Bubba pretty much summed it up. That's the easiest way to do it.
There are several ways to approach it, and your approach depends upon the conditions in place.
1. Is the mekugi ana already in place? (Often the smith will do this as part of making the blade.)
2. What material is used for the mekugi?
3. Will the blade be subjected to actual use (tameshigiri, etc.)
Hopefully your blade does not already have the mekugi ana in place before construction of the tsuka. If it does, you'll need to mark hole locations while the tsuka is still in two halves.
For reasons too detailed for this post, ONLY bamboo or delrin should be used for the mekugi.
You asked if the mekugi ana is supposed to be "angled". If you meant tapered, then yes. Ideally, all components in the assembly follow the same taper.
The easiest way to accomplish this is exactly how Bubba described. Keep in mind this requires a tight fit before drilling the mekugi ana.
If you do not have access to a tapered drill, then you can use a straight bit to drill the holes, then follow up with a tapered hand reamer.
Now to add to the confusion, there is another often-used approach, especially for "user" swords.
You may benefit by very slightly offsetting the mekugi ana toward the machi. An offset of 1/16" should be good.
This method would require an approach slightly more involved than the one above, but it's not difficult. If you need details on the best way to do this, just ask.
ALWAYS HAVE PLENTY OF SANDPAPER. IT'S ROUGH OUT THERE!