The wheel position is set by the bearing with the retainer ring. The other bearing floats in its bore, and gets forced against the spacer when you tighten the axle nut. You may have some rotating friction at first, but unless the bore is super tight on the floating bearing it will self-align after some riding.
Seat the retained bearing fully (use a tool that only hits the outer race). Tighten and stake the retainer ring. Slip the axle through the bearing, put the spacer on the axle, put the floating bearing on the axle. The axle helps align the bearing in the bore so it doesn't get jammed crooked. Tap the bearing in with the same outer ring tool, supporting the rim not the end of the axle.If you can push up on the axle with one hand white tapping with the other, stop when you feel the tapping in the axle: that means the bearings are aligned.