How to sync specific files with unison?

I originally [posted on SO](https://stackoverflow.com/questions/66462906/how-to-sync-specific-files-with-unison) but i realized this might be more suited here. I'm using [unison](https://www.cis.upenn.edu/~bcpierce/unison/) on Linux (Manjaro) to keep some files synced between two local folders but I'm running into a problem. I have a main notes folder which looks like this and has a lot of text files I write and export to PDF. my-notes/file1.pdf... file150.pdf I'd like to have some of these notes sent to another, more structured folder which I push to git.

organized-notes/
|
|------------------ Subject1/file34.pdf, file37.pdf
|
|------------------ Subject2/file11.pdf, file121.pdf
|
|------------------ Subject3/file97.pdf
|
|------------------ .git/

The issue is that unison works well between two directories or folders but I'm breaking down my files per subject and I would like them to be synced only in the relevant sub-folder. Also, I don't want to send all my notes to this more organized folder, only the specific ones I do select. Right now, anytime I make a change I have to cd to the relevant subject folder and use unison in there, like this unison ~/my-notes/file34.pdf file34.pdf. This is of course very annoying and I'd like to automate it. How I can fix this either with unison or another tool?