A lot of the configuration depends on your switches. But typically you connect one switch to another from whatever port you want. Gigabit devices support auto MDI-X. . In my small / medium business installations using broadband connections it has been...
NOTE: Each "|-" represents one level down. For example, devices following |-|- are connected to the device marked |- and so on.
NOTE 2: Depending on the application, WiFi Access point, Firewall, Proxy server, Security network etc... CAN exist as a single broadband / WiFi router. It is demanding a LOT of a router, but for example an Asus RT-N66u, or Buffalo WZR-600dhp with DD-WRT, either are up to the task for lower requirement networks.
ISP modem , network adapter, whatever your ISP calls what they use to connect your net to theirs...(Cable, DSL, FiOS, Google Fiber, whatever...)
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|- Business class firewall router. Make and model varies by need and budget of client.
|- Security network, proxy servers etc..
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|-|-WiFi access point. Again make / model varies. Can be SOHO class router with DD-WRT in access point mode.
|-|-Big Switch A. Servers. If space allows, workstations requiring fastest access to servers.
|-|-|-Big Switch B. Workstations requiring fast, but not fastest network access.
|-|-|-|-Big Switch C. Workstations, printers, and appliances having least requirement for bandwidth.
For the most part, crossover cables are a thing of the past. There are still a lot of old 10/100 switches out there that would need them, but gigabit has no need.