Some Xposed modules have own settings. If it has <category android:name="android.intent.category.LAUNCHER" />, it shows in launcher.
But I developed small module called QuickPic2Gallery -http://repo.xposed.info/module/com.pyler.quickpic2gallery. It has own settings but since "you set it once and you are done", I use for Settings <category android:name="de.robv.android.xposed.category.MODU LE_SETTINGS" />, so it doesnt show in launcher.
But I realize that there is UI problem. User don't know if module provide additional settings when you go to Modules tab in Xposed Installer. You need to click on module to see if there is Launch UI option (or long click on module)
I think the best solution here will be small settings icon in module textview to indicate additional settings.