Use u6.satisfactorytools.com/production to help plan Production. You can pick which Alternate recipes to use, and work out what you can output, and from what Inputs you’ll need.
Break things down into separate production pipelines, for more manageable chunks. Rather than build everything in one mega-factory, have smaller factories for grouped similar items, with similar raw requirements. Using the planner above, you can put Products from other factories as Input items.
Use Trains to shift resources around. This could be moving raw ore from a remote mine, to moving mid-tier components like computers to another factory for higher-tier things. (Later on you can use Drones!)
A more extreme way is to make mini-factory blueprints, and then just put down however many you need within a larger factory. You can make Heavy Modular Frames in one blueprint (using Iron Ingots, Steel Ingots and Concrete as inputs).
Reusable blueprints can also simplify the tedium of larger builds. eg; a Blueprint with 8 Constructors at a time, or 6 Assemblers, that you can chain together.
You don’t need mega-high throughput for many late-game items. Ignore the mega-factories popularly shown online.
Try to keep expansion in mind when laying out a factory. Have a rough idea on being able to scale it to 2x or 4x throughput (eg; building extra floors of the same layout, or stretching a manifold out to double-length).