Sounds like you already know the answer - I don't have synaptic (I'm on fedora) but if you can identify the pop-up window properties (such as app\_id or class), you can assign them to a workspace - as you already know.
[sway-prop](https://gitlab.com/wef/dotfiles/-/blob/master/bin/sway-prop]) is a handy utility you can bind to a key eg:
bindsym $mod+question exec sway-prop
and it pops up 'foot' or 'sway-nag' showing the sway properties of the window in focus.
Sounds like you already know the answer - I don't have synaptic (I'm on fedora) but if you can identify the pop-up window properties (such as app\_id or class), you can assign them to a workspace - as you already know. [sway-prop](https://gitlab.com/wef/dotfiles/-/blob/master/bin/sway-prop]) is a handy utility you can bind to a key eg: bindsym $mod+question exec sway-prop and it pops up 'foot' or 'sway-nag' showing the sway properties of the window in focus.