The question splits into two layers, the logical organization you fully control and the physical layout the filesystem manages and knowing which is which saves effort spent trying to control the wrong one:

The logical organization, entirely yours: folders and their hierarchy, naming conventions, where you put things, this is completely your choice and where organization actually happens for you. A sensible folder structure, consistent naming, a system by project or date or type, is the organization that matters for finding and managing files and it is entirely within your control regardless of the filesystem underneath. This is where to invest, since it is both yours to decide and the layer you actually interact with.

The physical layout, mostly the filesystem's job: where files physically sit on the disk, in which sectors, how they are fragmented or contiguous, is managed by the filesystem and not something you directly choose, nor generally something you need to, since modern filesystems and SSDs handle this well and the days of manual defragmentation mattering are largely past. Trying to control physical placement is usually effort misspent.

What you can influence at the physical level, the useful exceptions: partitioning divides a drive into separate volumes you organize independently, useful for separating system from data or different purposes, which is a real organizational choice. Choosing where to install versus store data, system on a fast SSD and bulk files on a larger drive, is a placement decision you make. And filesystem choice at format time, NTFS versus exFAT versus others, affects behavior and compatibility, a deliberate choice for a drive's purpose.

The practical framing: put your energy into the logical organization, a clear folder structure and naming system, which is fully yours and does all the real work of keeping files findable and manageable, use partitioning and drive assignment for the coarse physical separation that genuinely helps and let the filesystem handle the sector level physical layout it manages better than manual effort could. The organization you can and should choose is the logical one, and it is also the one that matters.