Australian citizen living in Germany, need a chinese visa!

Hi, I am an Australian currently living in Germany and desperately need to sort out a chinese visa. I have the application form and photos and copies of hostel information and flights. I am flying from Frankfurt to Mongolia for 2 weeks and then flying to Beijing for 1 week. I have my Mongolian visa already done in my Australian passport, I have 2 questions:

I have an Anmeldebestatigung for my residence in Heidelberg to prove my residence here in Germany, is that enough? I also have a german passport and that is why I can stay in the country but when I went to the Frankfurt consulate last time as soon as I showed them my german passport they got confused and said I had to get it in there. I am sure I should be able to get it in my australian passport as that is the proof of my residence in Germany?

Also... I don't want to get the visa in my german passport as the mongolian one is already in my australian. If they dont let me get it done in my australian passport for some reason and I have to get it in my german one, can I travel into and out of mongolia on my australian and then present my german when I get to China or will they get suspicious? I just dont know what to do as it has been 3 weeks of people telling me different things. I need to sort this out and it very complicated and I need some advice.

Anything you can tell me would be great. Thankyou.