With iron sights, I would definitely sight in at 25 yds. You won't be doing much other than plinking beyond that range with irons if you're like most shooters.
To start, shoot at about 10 yds onto paper with an big "X". Seems pretty darn close with a rifle. You should be able to almost look down the barrel and eye ball it. Adjust to be near bull then move out to 25 yds and do the same. I would leave the iron sights set for 25yds. Do essentially the same thing with the scope, but move the target back to 50 yds once you are close at 25 yds and adjust it.
For scopes, I have read that the optimum distance to sight in is around 50-60 yds. There is no difference with iron sights, but I shoot at what I can see well at that means 25 yds with irons or 4x scope or 50 yds with a higher powered scope. Use the table above to estimate point of impact for the other distances.
Once you are sighted in with your scope, shoot at the various distances holding for the bull and just observe how the impact point changes.
There will be a couple of inches difference in the impact point at 50 yds with standard velocity vs high velocity ammo.
If you are having trouble, some gun shops will do the bore sighting for the scope for free if you bought the scope from them. Make sure the scope is "tight" on the rifle. If it is loose, you will never get the rifle sighted in.