I am a relatively uneducated (music theory and process, anyway) composer. I have recently been working on arranging a piece that gave only the melody and the expected chords. I have been working on it and working on it. I have Sibelius review it by noting parallel 5ths and octaves (because, while I often can hear it, I can't seem to identify the offending notes), and when I fix one, and two more popup. References to books, etc. and any personal habits and workflows would be appreciated. Thanks!
Turn that feature off if you can.
The rule of 5ths and octaves is a rule that came about around the time that the major and minor third was declassified as a dissonant interval in church music. Prior to that in Medieval times all church music was sung in what was called Parallel Organum 4ths, 5ths and octaves because they were considered the only perfect intervals suitable for God's worship.
Okay in the age of enlightenment the 3rd was allowed and to distinguish the "new" music from the old church stuff a rule was devised outlawing consecutive (parallel) motion of 5ths and octaves (and even 4ths as the 5th inverted is a fourth). The reasoning was that those intervals in parallel especially in two part writing would stand in stark contrast to the new style of music. Like you'd be going along in 3rds then 5ths and octaves would jump out at you reminding people of the old days.
From that a whole set of rules of counterpoint crept up governing 2,3 and four part writing in Church music. So the question to ask yourself is are you writing 18th century chruch music. If the answer is yes, then follow the rules, if your answer is "no" then forget about it.
All that, it's a thing of the past. It really, really is. But, from counterpoint a few good general rules came up that apply today. Firstly, is the idea of good voice leading. Finding the smoothest way of going from one chord to another. The other is chord voicing. A way to vertically arrange tones in an efficient and sonically pleasing way and a few other good rules and guidelines. Another is to a greater or lesser degree 2,3, and 4 independent parts commonly arranged today as bass, melody or lead and accompaniment.
So counterpoint is a good study but only from the perspective of what is good and ignoring what I call the "thou shall nots" of counterpoint. i.e. Thou shall not place octaves and fifths consecutively you bad bad bad boy. That is intended as a joke but if you read Fux counterpoint that's basically his argument.
That being said, good part writing is far more important than paying attention to stultifying rules that only hinder creativity because some monk back in the 17th century decided to make some stupid rule governing the use of 5ths and octaves in music.
So practically speaking if the parts are good, strong melody, good bass lines and good middle parts and the parts progress in a smooth way (unless you want to shock for good effect buy having parts jump out which is valid) and the voicings are good then don't worry about parallel motion.
Here's an example. I wrote a little choir piece a while back that breaks every counterpoint rule known to man, but it still sounds decent enough, though I wasn't too happy with the performance.
I will just soldier on with my training and keep working it over. 
