Bookmarks are stored as files. If you wish to specify the path to agregore set the appPath property in your .agregorerc config file. You may need to do this if you've moved an agregore AppImage to /usr/bin for example.
This can be done by pressing ALT to bring up the menu and then clicking Help > Edit Configuration File, then adding in the following contents:
{
"appPath": "/usr/bin/or/wherever/agregore-browser"
}