Ok, you've got two options, do you want a skunk stripe or not? Skunk stripes were usually used for necks that didn't have a separate fretboard (all-maple necks on fenders). If it's your first build, I'd go with a separate fretboard, it's the simplest solution.
If you don't want a skunk stripe, then you take your neck blank, rout out the truss rod channel in the centre to the right depth (not all the way through), then glue the fretboard which is a separate piece of wood to the top of that, sealing off the top of the truss rod hole.
If you do want a skunk stripe, then rout all the way through the neck blank, creating a slot down the middle that's the length of your truss rod. Then glue in the skunk stripe in the bottom, making sure there's still a slot the right depth for the truss rod. Then once that's in, you've got pretty much the same situation as in the first option, drop the truss rod in the channel, and glue the separate fretboar on top.
This is easiest if you're using a double action rod like a StewMac hot rod, which needs only a straight channel. Makes life much simpler than routing a curved one. Trust me, for your first build, use a straight channel rod.