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How to set up a system with two hard drives?

I have multiple systems, each of which has two different hard drives: one fast SSD and my good old spinning rust.
Originally, I had set up the drives to have my root directory `/` on the SSD and my home directory `/home` on the rust.
Despite this setup, my systems became sluggish a few years ago.
This is when I learned that there are a bunch of files (e.g. in `/home/$USER/.cache/`) that various programs need to load.
Because these directories were on the rust, programs became slow and I decided to change things up.

On one system, I ended up creating a `/data` partition on the rust and created symlinks for directories that are user-data heavy (e.g. `/home/$USER/Downloads`) to this `/data` partition.
On the other, I didn't want to spend time moving big files around and decided to remove certain system directories to a new directory `/fast_home` on the SSD and linked the removed system directories to this new directory.

Although both setups (still) work pretty well, they do come with some small annoyances.
 1. I can not move any of my user-data files to the Wastebasket. Every time I want to delete a file, I get a warning that the file will be lost forever. I learned to live with that and I am aware that adding a `.Trash` directory somewhere should solve the problem, but I was/am too lazy to fix it and I kind of dislike the asymmetry of having a (nicely hidden) trash directory under `.local/share/.trash` and one in the root of my user-data directory. I am happy to learn about alternative workarounds.
 2. Some programs do not play nicely with the symbolic links. One notable example is when I am trying to debug a file that I have opened in an editor or IDE. When the file is behind a symbolic link, the editor will believe that the file is under `/home/$USER/Documents/file`, but the debugger will refer to the file `/data/Documents/file`. Clicking on the filename in the debugger output will therefore typically open the same file again in a new tab. Similarly, I had scenarios where certain files ended up in one of the system directories leading to similar problems. Is this just a misconfiguration issue on my side?

Soon, I will be getting a new system and it is most likely that I will have a similar setup.
I presume that most people have a similar setup, but I fail to find some kind of agreed-upon standard to set up this kind of system.
At least most tutorials/guides seem to suggest something similar to what I have already without addressing the annoyances that I am experiencing.

That brings me to my question: What (well-established) options are there for setting up dual drive systems and what advantages/disadvantages/workarounds do they have compared to each other?

PS: (in case it might be relevant) I am on Arch Linux with Gnome, using Code (OSS) and various JetBrains IDEs.