Получилось
Через xrandr узнаем какие мониторы у нас подключены, и потом запускаем программы на определенном мониторе.
Вот мой полный конфиг
exec_always --no-startup-id lxpolkit
exec_always --no-startup-id /usr/bin/skypeforlinux;
exec_always --no-startup-id /usr/bin/google-chrome;
exec_always --no-startup-id /usr/bin/copyq;
exec_always --no-startup-id /usr/bin/local;
exec_always --no-startup-id /home/serii/.local/share/JetBrains/Toolbox/scripts/phpstorm;
assign [class="bomi" instance="bomi"] → 1
assign [class="figma-linux" instance="figma-linux"] → 1
assign [class="Code"] → 2
assign [class="jetbrains-phpstorm"] → 2
# assign [class="Google-chrome"] → 1
assign [class="Skype"] → 4
assign [class="Slack"] → 5
assign [class="firefox"] → 5
assign [class="Local" instance="local"] 6
assign [class="TelegramDesktop" instance="telegram-desktop"] → 7
assign [class="qBittorrent" instance="qbittorrent"] → 8
assign [class="Audacious" instance="audacious"] → 9
assign [class="Gimp" instance="gimp"] → 10
workspace 1 output VGA-1
workspace 2 output DP-2
workspace 4 output DP-2
workspace 6 output DP-2
# for_window [class="figma-linux"] focus
for_window [class="Skype"] focus
# for_window [class="Slack"] focus
# for_window [class="firefox"] focus
for_window [class="jetbrains-phpstorm"] focus
# for_window [class="Code"] focus