Really difficult, there are many reasons why a mother can kill her joeys, they can sense the joey is sick, they can lack milk to feed both so choose to reject one, and so on.
If she is alone to raise the joeys, it's more difficult for her, the father would normally take care of the joeys when she is out to eat and exercise, which can explain why she sometimes leaves the joey alone and sometimes brings him along.
One thing is., does she come to check when the joey is crying? If you don't hear him crying at all, or don't see him trying to crawl out of the sleepåing pouch, he is likely fed.
The fact that he seems skinny might mean that she was lacking milk to feed both of them properly. In any way, removing him from his mother is not necessarily a good idea, unless you observe clear signs of rejections. What you can do however is check often, and if he keeps being underweight, increasing the mother's protein intake, and maybe supplement the joey by adding some hand feeding with wombarro milk replacer or similar products.