I will assume you can mark the location of the holes accurately, and your
concern is (as you did note): how to drill the holes accurately.

Use a brad point drill bit, of the right size for your shelf pins or
sleeves.
This type of drill bit has a sharp point to easily start your hole where you
want it to go.

Use a Drill Stop to limit the depth that you go so you do not blow through
the side.
Also, be careful to hold the drill steady and at a right angle to the board
being drilled.

Check this out: http://www.woodworkingtips.com/etips/etip021011wb.html
it is a drill stop and right angle helper.

Practice a few on a scrap bit of wood to make sure you have it right & are
comfortable doing it.


Matt