How many sidings, industries, and towns do you have?    What’s your average train length?
When I first started, I had one yard, a staging area, and two towns.   One of the towns had an interchange and 3 industries on 3 sidings.   The other had 4 industries on 4 sidings.   I had about 25 cars at the time and limited my trains to no more than 5 cars between yard, towns and staging.   I decided 2 trains would be appropriate, one in each direction.   I’ve since added additional industries that I use to block the passing sidings. 
I used MS Word to build a setup list telling me where to put  the cars at the start of a session.   Then I manually created a switch list for each of the two trains.   Finally, I created a Final list showing where all the cars would be at the end of the day, assuming both trains ran.   This I would use as a starting point for the next operations session that I would create.
The advantage of this method is that you can control everything.   If I want a car to stay with the train the whole time, it’s easy to do.   I can set up different switching challenges and even specific moves within a town.   Because I save it as a single document in Word, with 4 separate pages, I can use it again and again when different people come to operate.   Over time I can build a set of sessions to use.
The disadvantage is that there is not as much randomness or unpredictability that I get with a computer program.    Something like TrainOps will generate demand based upon factors that I set up for an industry.   Thus, sometimes my train may be at full capacity, other times I may have only a few cars between towns.    It’s also a lot of work to set up, as you need to make sure that each car is only moved once, if at all.
I found RailOp to be way too complex for ME and my little two train railroad.   I know Ric uses it with great success, as does Fred on his IPP&W;  but they may have ten or more trains running in a day.
Personally, I’d look  for something that requires only one sheet of paper while operating; that’s why I like the idea of a switch list.
There are some others that I looked at:  Ship It, ProTrak, Interchange, Minirail and probably some others that I’ve forgotten about.   I found that most of these are designed for the smaller scale layout with several hundred cars and the ability to leave everything out between operating sessions.
For overall design I recommend  http://www.gatewaynmra.org/operate.htm and http://www.opsig.org/  The OpSig has a $5 per year electronic subscription that I find very handy.