Thank you Ters and Leartin for your detailed info. The way I set up my network almost always leads to the situations you've both described of one route, usually not the one you intend becoming the "Main" route for passengers and gets overloaded.
I adjusted this problem by "adding" stops and truncating routes in junctions. I'll have to post some screenshots later of specifically what I'm talking about, but I'll attempt to describe:
I have several different type of train services that will run on a single trunk line say from Terminus A to Terminus B:
ICEx (Intercity Express) The initials I place in the line manager window for ease of locating. A - B nonstop
This type of service only usually stops at major termini or junctions (no more than three or four stops max), fastest most direct service between A and B
IC (Intercity): Stops at more intermediate junctions or where lines cross (usually limited to 5 to 7 stops)
A - 5 - B
R (Regional): If the trunk line is set up like this: A -1-2-3-4-5-6-7-8-B, with the numbers being local stops, I'll set a series of R trains to cover certain portions of the line usually radiating from the nearest Terminus, so for example: R train one would go A -1-2-3-4-5 and R train two would go B-8-7-6-5. Both trains meet up at station 5 and that would become a "Junction" station where an IC or ICE train would a halt. If I had, as I used to do, a single stopping train calling at all the stops between A and B, I would get results as you guys were talking about. I've found if I break the lines up into segments, I can force pax onto either IC or ICEx trains. The naming scheme I borrowed from European train classifications as in the US, we're lucky to have a train at all, nevermind what "type" it is!
B (Branch) These short lines usually radiate from junction stations and will connect with a Regional or, depending on size of the city/passenger numbers, an IC train.
I've done my best using this system to avoid the pitfalls of the way the Pax route themselves over the map and I think it's working so far. I started this thread to get a much better understanding of the mechanics behind it and to see if what I was going would be a decent work around. I usually still end up with stations that are WAY, WAY over their capacity for passengers at junctions and other locations, but I don't necessarily mind this. I play more for creation than actual profiteering (per the game).
Again, I'll try to post some screen shots of my network for clarification of what I'm describing above.
Thank you guys for your input!