If it's Saturn, you need to make sure you have a strong Pineal chakra and general mental acuity and force, first. You have to be able to overcome whatever a Saturn square throws at you, and that actually depends on firstly and is cultivated in the Mind (The Solar Plexus being important for the Will part).
If it's Mars, which I don't think should be considered a Malefic, then it would also be the opposite polarity which is Venus, if Mars is causing issues like over-assertion, carelessness to others and whatnot. This same energy form is very poignant to human nature, so even just the act of meditating and self-reflection (Pisces as it precedes Aries) will enable a person down the line to correct whatever issues it is causing.
If it's Neptune, the answer is Mercury. You would also want to place emphasis on the lower chakras and like for Saturn, the Pineal chakra as Neptune is deceptive. The key for Neptune is essentially just meditating to keep it in check and other than that it will always act on you in a mostly benign way which you don't have to notice. Empowering planets that are affected by Neptune will overpower and break it, turning it into this benign influence. Empowering houses which are affected by Neptune also make it a benign, "enriching" influence instead of a weakening one.
Now properly answering this. If the houses are suffering, and you empower the planets within them which you believe are causing this, unless you will it in a way which is benefic, it will cause issues. The key is the ruler of the house, empower that planet with squares, and if the house ruler is one of the outer planets, then empower their functions (runes associated with them, meditation of Neptune, for Scorpio you can do Mars, Aquarius-Saturn, Pisces-Jupiter etc.) as obviously squares are dangerous for those planets. If the house ruler is placed in its own house in its own sign, then working on the planet will be beneficial for that house even if its malefic, but make sure it's in its home and going over that same point (like a Saturn return) so you don't muddle it's natural energy there. According to KRSastrology, when you have a house ruler placed in its own house in its home sign, it becomes "protected" or in other words makes sense energetically. I have faith in this idea, observing the chart as a diagram of patterns and processes, it does make sense. For Malefic planets this is therefore quite interesting, I wonder how the dynamic of this plays out in a person.
But if it's not in that state then yes, empower the house ruler itself, not the malefic planet. Doing actions throughout the life as an SS, which pertain to the affairs and expression of that planet will write itself at some point sooner or later. The house affairs itself are connected though, to the ruling planet and also any other planets it makes tight aspect to. If you want to improve the house you improve those.