Welcome to the Grammar Exchange, Skytj. May I ask where you are from, and what your native language is? Sometimes knowing such things helps us understand your difficulties, because your native language is bound to have constructs that don't translate exactly into English, and vice versa.
I usually would not insert a preposition between the phrase "spend time" and a present participle. I would say that I need to spend time working in my garden, not that I should spend time on/in/through working in my garden. I can possibly imagine an exception for something like "I should have spent a little bit more time on fixing the roof", but even there, if the "on" is acceptable, it's certainly not necessary, or even preferred.
I can't think of any instance where "in", "by", or "through" would work in such a construct.
As always, I welcome the opinions of my esteemed colleagues.