Traditionally if the "it" was general or indistinct, feminine hi was used. This is still the case in more formal language and has continued in the colloquial language in certain circumstances, such as when telling time (Mae hi'n dri o'r cloch "It's three o'clock") and talking about the weather (Mae hi'n bwrw glaw "It's raining"), and in certain phrases, like Cer amdani "Go for it" (lit. "Go for her") and mynd ati "go to it (and do something)" (lit. "go to her").
However, the tendency in colloquial language today is to use masculine fe (south)/fo (north), for example Dw i ddim yn gwybod beth i wneud amdano fe "I don't know what to do about it" (lit. "him").
So my advice would be to use the masculine for something general, vague or indistinct unless you're talking about time, weather or using a set phrase or formal language.