It is hard to know where to start with such a huge topic as this. How much do you know about prototype railroads? A lot of good ideas can be gleaned just by being an active and informed railfan.
I suggest investing in Tony Koester's fairly new book "Realistic Model Railroad Operation: How to Run Your Trains Like the Real Thing." I think John Armstrong's book on Track Planning for Realistic Operation might also be very interesting to you.
Dave Nelson
A very good reference on what the full-size railroads do is Armstrong's The Railroad - What It Is, What It Does. It helps to know what the big guys are up to if you're trying to imitate them in miniature.
There are many different operating schemes for model railroads, ranging from simple and straightforward to labyrinthianly complex. Mine tends toward the latter - but that may be because I've been developing it to very specific parameters since 1964.
Whatever technique you eventually choose, I hope you have as much fun as I do
Chuck (modeling Central Japan in September, 1964)