as long as you remembered to put your spacers back into the rear wheel, you should be ok that way on the side to side alignment.
so, as you probably noticed, the alignment marks from the factory are notoriously bad. there is the string method, but i don't put alot of stock in that...you have to have the front wheel perfectly straight for it to be accurate.
there is a tool made with a slider bar and two pointers attached that can clamp in place. you measure from fixed points, such as the swing arm pivot and the rear axle, which are equidistant on both sides of the motorcycle. that's the easiest way to be sure you've installed it completely in line.
if that's not available to you, find a road without a crown to it (a crowned road will make you're bike feel like its pulling to the right), and start your adjustments. get going a decent clip, nothing dangerous, but 40 +/- should work. make sure you're centered on the seat and sit up, let go of the bars. see which way it wanders. for a right pulling motorcycle, you'll need to back off the left side or bring in the right (pick one, don't do both). go with 1/4 turns in the adjustment nuts (or 1/6 turns if its easier to keep track of the flats on the faces), until you're in the right place alignment wise, then readjust equal amounts on both side to set your chain slack (you'll need to after that).
sorry for the lengthy explanation and over simplifications.....maybe it'll help some people who aren't sure how to get that done....