When people use "どうしたもんかね," that means that they suffer from or are worried about a difficult situation that they cannot figure out how to overcome. Therefore, in this context, the translation will be "What is difficult is our current situation." The Japanese sentence includes a content that the speaker talks about him and his younger sister, but probably, I can guess that he already mentioned something about her as his sister in the former sentence, so you can omit that part when you translate it. I hope this helps you to understand the sentence more.