I got a laptop recently where I installed Arch / Hyprland (not Omarchy) but I know what you mean about overlapping windows. I do this all the time on Windows where I overlap windows and then toggle some of them as "always on top" to optimize whatever workflow I'm doing at the time.
The good news is Hyprland supports this quite nicely. I don't know when you last tried it but it's easy to float windows as needed in a dynamic way. You can assign a keybinding to toggle floating on a specific window and then you can move and resize it while holding either mouse button.
It also has a feature called "pin" to make something always on top which you can assign to a keybinding to toggle this as needed. Floating windows are already pinned by default on top of tiled windows so you only need to deal with this when you have 2+ overlapping floating windows.
Combining floating and pin together lets you overlap things in whatever way works best for you in a config-less way.
Optionally you can also pre-assign specific apps to always float or be pinned in your config file and toggle them with keybinds too.
The good news is Hyprland supports this quite nicely. I don't know when you last tried it but it's easy to float windows as needed in a dynamic way. You can assign a keybinding to toggle floating on a specific window and then you can move and resize it while holding either mouse button.
It also has a feature called "pin" to make something always on top which you can assign to a keybinding to toggle this as needed. Floating windows are already pinned by default on top of tiled windows so you only need to deal with this when you have 2+ overlapping floating windows.
Combining floating and pin together lets you overlap things in whatever way works best for you in a config-less way.
Optionally you can also pre-assign specific apps to always float or be pinned in your config file and toggle them with keybinds too.