I didn't thoroughly read all the responses so if this repeated, my appologies...
When you're lining up for landing, what are you focusing on? The end of the runway closest to you? You may find it easier to "see" your alignment if you focus on the far end of the runway.
Your eyes can better determine "alignment" under what your looking at rather then on top.
I was talking more about judging your glideslope rather than alignment, but no, if you focus only on either end, you will not do very well. The entire runway, initially, has to be considered... and the same rule applies to some extent: the two ends of the runway should not be moving laterally relative to each other. Approach end should be going down, departure end should be going up.
Just keep the two ends aligned vertically... it's that simple.

Again, it's a matter of practice, and there's no sure-fire trick to guarantee perfection. It's like trying to describe in words exactly how to juggle three balls, or something like that... can't really learn how to do that from someone else's description.