My bitch is still cleaning up after her 5 weeks old pups which i know it means shes a good mum. I pick up the poop through the day or try and let them go on the decking before she gets to it but i know she cleans up at night And tries to get the ones on the decking when I'm not looking. Problem is she is being extremely sick after it and its poo that shes bringing up. Question being can i separate her in another room through the night?

By 5 weeks, my bitches were usually not sleeping with their litters.   If she's being sick after cleaning up what the puppies produce now, then for sure I'd not have her with them so she can get to their pooh.