Good idea! It would be nice that I provide a portable way to do it. Right now, here is what you can do:
The install script of a quest can try to edit the settings files of the launcher GUI. On Debian or Ubuntu systems, I am pretty confident that it is always ~/.config/solarus/solarus.conf. This file looks like this:
[General]
last_quest=/home/christophe/jeux/zelda_roth_se
quest_fullscreen=false
quest_video_mode=normal
quests_paths=/home/christophe/jeux/zelda_mercuris_chest, /home/christophe/jeux/zelda_olb_se, /home/christophe/jeux/zsdx, /home/christophe/jeux/zsxd, /home/christophe/solarus/sample_quest, /home/christophe/jeux/zelda_roth_se
video_acceleration=true
You have to grep the quests_paths line to see if such a line exists and if the quest is already present.
And if the config file does not exist yet, you can just create it as
[General]
quests_paths=/usr/path/to/quest