I place a straight edged ruler against the rear sprocket under the top run of the chain.
By looking along the ruler, I can see if the chain travels straight. If it is straight, the rear wheel is aligned.
If the chain travels straight, that does not necessarily mean that your wheels are aligned [and vice versa]. You have a few options:
1) Try to align the front and rear wheels - this should assist handling
2) Try to align the front and rear sprockets - this should assist chain and sprocket life
3) Something else
Doing #1 does not necessarily mean that #2 is a byproduct and vice versa. However, if #1 or #2 is a result of the other, that is great! If the frame, swingarm, fork tubes, fork tube clamps, etc. are bent/twisted, you will probably have a difficult time achieving #2 from #1 and vice versa.
One person's "never had a problem" may be someone else's "problem" as those are relative terms.
I am not saying which method is "best", as it is up to each person to decide what they want to do.