One thing you might want to try with her bed (cause you said that is a plush) is maybe put a plastic liner on the top right now while she is so young. Because it is plush, the liquid may just be getting soaked up and that may just be enough for her to tolerate it. But if you put on the liner it will not soak up and she will be forced to lie in it. She won't like that all
That might help her get the message to try to hold it in or let you know somehow that she has got to go.
As far as the crate goes, if you don't like her being there for long period of time (7-8 hours) As she gets older and the more trust her. Open more space off for her very slowly. Use Xpens, baby gates, etc....