for 'what are you doing now", mostly it depends on lots of things like feelings, intonations. as for me, it would be a big challenge to explain how they work. there are more than two ways to ask somebody that. here are some of examples, and all are informal. 지금 뭐하고 있는거지? mostly, it could be used when you are talking to yourself complaining about something. 지금 뭐하고 있는거야? sounds like somebody is upset a bit compared to the following two sentences. 지금 뭐하고 있어? 지금 뭐해? these two sentences have the same meaning, but '지금 뭐해?' is a bit aggressive but not that much. i'd recommend '지금 뭐하고 있어?" for 'what are you doing now". it's the most natural and common in spoken. just my two cents.

Between 거야 and 거지, there is hardly difference in meaning, so that you can use these words on the same occasion. You should be digging into the structural study of those, which is quite difficult to explain XP if you wanna know the fine differences about them.