If it is obvious in your evidence that there are separation(s) of several weeks, for no compelling reason such as work or study commitments, during the time when you are trying to demonstrate that you are living together, then it will not look good to INZ. Remember that partner-sponsored visas, being the ones with only one category of required evidence, are the ones most targeted by fraudsters using people paid to lie to get them a visa, which means that INZ scrutinize every application very carefully under the assumption that you COULD be liars. To get quick and easy processing of a visa, you need to have plenty of evidence of the presence of both of you in the same place, week by week.