Even if the house is empty, the transit will have an effect. This is in relation to the subjects related to the houses in question and the nature of the transiting planet.
The stars must be in aspect with the planet to "give" a predisposition. In case of bad aspects/positions of stars or degrees, through meditation and the help/guidance of the gods, they can be mitigated and/or sublimated.
which meditations would it be freeing the soul? i don't think it's a good idea to do squares bcos many of mine will just amplify certain problems rather than help
So Astrology is kinda complicated but i will try to explain as much as i can;
Every planet and sign rule diffrent houses. For example Aries and Mars rule over the first house in our natal chart. For example let me say you have no planet in your 1st house but it is in Libra. Then you should look at the placement of ruler planet of Libra, which is Venus.
In your occasion, you have Gemini in your 9th house, ruler planet of Gemini is Mercury and ruler planet/sign of 9th house are Jupiter/Sagittarius. You have to look for those signs and planets placements in the first place.
so in the case of my gemini, it is the same logic as usual but in relation to the ruler planet (mercury) instead. So the properties of the transit planet will mix with Mercury in this case? as well as the traits of Gemini?