Sounds like a complicated situation. Separating bonded chins is going to be very stressful for them and sometimes it can result in extreme life-threatening depression in one or both.
You will need to separate them as soon as the female delivers in order to protect the kit and prevent breeding during post-partum heat (breed back). If you think delivery is imminent you can probably block off the two level cage with a divider. When the female delivers she really doesn't need any special accommodations but the kits will be able to escape from bar spacing any more than 1/2" by 1". Some people use construction cloth with that bar spacing or 1/2" x 1/2" and cover over the bars with it but it might be better to just get a cage that will work with long term plans on keeping a second pair of chinchillas in.
Hopefully there will be one female kit that you can keep with the female and you can try to pair the male with another male. It is very difficult to pair a female with another adult and it's not always possible. Males are much easier to pair with other males but that is not always possible either depending on several factors. Pairing them with other chins can prevent or reverse depression but not always. Do not try to pair the female with an adult until after the kits are weaned.
I strongly recommend removing the ladders in the cages. These can be dangerous and, as you can see, the chinchillas prefer the space to jump around in.
Here are some articles you may find useful:
http://www.chinclub.net/qna/mojofaq.cgi?cat=preghttp://www.chinchillaclub.com/forum/index.php/topic,4000.0.htmlHope this helps.