I don't like to level off the scope cap, I prefer the bolt raceways. I then sight the plum line through the bore and snug up the vise. Line up the reticle to the plum line. When the reticle is on line and the bore is on the line, you're GOLDEN, your scope is aligned to bore, somewhat a rarity in factory rifles and/or mounting components.
Before I do all this, I check the rail for fit and bed if needed. On direct mount rings, I mount alignment bars to check if scope will align with barrel. One bar has an aluminum 24" rod insert that should align with barrel or show the amount of offset. If everything is straight I'll go to my mounting procedure. If not, Burris Signature rings w/inserts can help. You do not want to use all your windage to zero a scope. Using custom actions, I rarely have to use more than 2 moa to set windage zero.
My method, maybe it will help.