You may want to try the wikepedia site, it has some basic history and background. There are a variety of commodities transported by "piggy back" (wheeled trailer on flatcar, or tofc) and containers (single or double stacked on flatcars, or multiple segment container cars (container of flat car, or cofc).

High value items from tennis shoes and electronics, to low value items like used newsprint can be in any of these containers or trucks, with everything else in between. Containers now mostly have rfid type technology to locate and track shipments. Shipments are sorted and prioritized based on destination, cargo types, time sensitivity, and contractual requirements with shippers, with higher value and perishable items generally having higher priority, who pay more for that service "quality", over say lower value shipments of rebar or used newsprint exported to Taiwan, seeking the lowest most cost effective tariff. So there is definitely a rhyme and a reason for how its done..

Intermodal has essentially replaced the boxcar, requiring a siding, and a switch, and train make up and priority will vary widely, as it did with boxcar traffic. Many railroads run true "unit" intermodal trains for customers like a UPS train, or a Maersk train, or even container "auto parts" trains for delivery to auto assembly plants, serving as a conduit for everything from ocean shipping to package delivery. And, some trains, are made up of whatever general intermodal traffic is going to a given destination. How much is a customer willing to pay, and what level of reliability or speed of delivery they require, is a big part of what determines priority.

RR's are increasingly competing for truck business of over 500 miles, and last month, intermodal loading set a record, surpassing carload volumes (as intermodal continues to grow, while carloads of coal have dropped off, significantly). Intermodal train priority and operations reflect these factors and will vary widely by origins, destination, route conditions, connections, the customer base, and what is being shipped.

Train size, train power needs, train weight, route capacity issues, and other operational considerations also affect how all trains are put together.

It's not a simple answer, but I hope this helps some...