I recently assembled Leupold mounts and bases on a Remington 700. This particular base is a two piece, and the rear base has screws on both sides. You are supposed to twist the front base into the mount, then tighten the screws on the rear base. whch clamps the mount to it. First, I wasn't sure that I had the front sight perpendicular to the bore, but I eyeballed it as best I could. Then I put the scope on and I was sure that it was NOT parallel to the bore. So I adjusted the screws on the rear base until it looked right.
I kept looking at it all afternoon, wondering if it was straight.
Today I took it to the range. At 25 yards, impact was two inches to the left. I attempted to adjust this by the screws on the base, making what I thought was a gross adjustment. I fired with no change in impact point. I then sucsessfully adjusted to the center with the knobs.
At 100 yards, impact was two inches right. Again, I was able to zeero with just a few more shots.
Is there a simple way to be sure your scope is lined up? And an even dumber question, is it critical?
To my reasoning, which is somewhat suspect, if the weren't lined up, your impacts would be left or right up to a certain point, then what was left would start going right, and vice versa.
What's the scoop?

www.brownells.com/aspx/NS/store/ProductDetail.aspx?p=833&title=SCOPE+ALIGNMENT+RODS
Here is a product from Brownells.

2 inches is not a gross adjustment thats about 8 clicks..
just bore site it at 50 yards,tighten the screws down,on both sides then fine tune it with the knobs,....I have been 4 foot off at 100 with no more "clicks" ...thats when you get that pucker feelin.....WTF....

I've had good luck with holding the rifle in something like a rife vise, pulling the bolt and looking through the bore at a distant object, then adjust your scope.  You should also look at a verticle object like a string with a wieght attached while the rifle is leveled, this will show you if you need to rotate the scope within the mount.

the last rifle i boresighted was less than an inch high at 100 yards. that is the way to go i think. but i guess i get to use the bore sighter for free at work.

A long wooden dowel (2 or 3 feet long), laid in the lightly snugged scope rings will quickly show you the extended axis and how it compares with the bore.  

My father is a retired machinist and he made me two 8" long by 1" diameter brass pins tapered to a fine point on one end.  For the two peice bases I line up the points after that I lay the scope in the bases and snug down.  Check with a bore sight, then to move windage wise I turn the front base using the pin point as a guide as a reference and then realign the rear pin and check until windage is good.  Seems like a lot of work but it eliminates torque on your scope tube.  Also I have forun that the two bases or rings are not level with each other in some cases.  So my dad made me a 14"x1" bar that I use with lapping compound to lap all my rings level.