The rim should center directly in the middle of the hub. The hub flange R/L distances in relation to this middle point is what you will base your spoke lengths on and will also be the center point for the rim. Spoke hole diameter on the flange (on which diameter the spoke holes sit) is also a critical measurement in determining your spoke lengths. The actual spoke hole diameter is also necessary but not so critical.

The first build is a bit of stress. It gets easier.