Junan, basically you get warnings along the lines of 'such and such is starting to feel cold/hot, you might like to get them indoors, on the hot/cold days. Basically get them indoors on cold days, and while they are out, ensure they have their winter outfit on.
I think it is space rock possession, not gem possession that attract the aliens. From my experience, aliens didn't really prove that much of a problem for me, i think I only had a male pregnancy once from alien abduction, although there were many more abductions of males and females from among my family.
I found the freezing of lakes and of outdoor plants during winter and some spring and autumn days to be much more annoying than the aliens, so much so that I no longer play with the seasons expansion pack.