Jerome,
Your opening statement here indicates you have a good start in knowing what you want and including what you have. Running a model railroad like a real railroad requires a lot of patience to identify the full range of features you wish to employ. For example, do you want signalling and CTC (Centralized Traffic Control), or do you want something more old fashioned (train orders, track warrants and dispatchers)? What kind of system do you want to use to control the movement of railcars? Are you going to include passenger operations or a "fast clock?" Or will you create a hybrid system that only uses attractive (to you) parts of any of these features.
There are numerous model railroad books that deal with this subject (operations vs. "running"), and it also helps to become familiar with the habits of the railroads (prototype) you will be modeling through reading more books. With respect to combining postwar Lionel with modern Lionel, some will say pick an era (1930s or 1940s) and model it while others will say do what you wish. My philosophy is: It's your hobby and your railroad, so do what you want and enjoy it. Others may not like it, and some may be very critical, so develop some thick skin to avoid the drama.
SCARM, like all programs, is a tool. Go to their website and look at the tutorials to see how it works. Then, come back if you have specific questions.
For designing your layout, again, there are numerous publications (I usually read something from Kalmbach by John Armstrong or John Allen) designed to help you get started. First, though, learn how to draw your available space in SCARM along with all things you have to clear or avoid in your train room area. Then decide whether you want pure point-to-point operations (like most real railroads, start somewhere and end somewhere), some loop running to keep trains running while you switch cars at an industrial complex or passenger station, or a hybrid like a point-to-reversing-loop operation.
Search through this forum for any of the terms I've used above that you don't understand, and if unsatisfied with what you find here, try googling the term. For the size layout you are planning, it is certainly wise to do some reading and research before you begin spending money.
Good luck and let us know how it's going.
Chuck