Me again....... more questions!!

So..... Willow has now been in our house for 2 weeks now. On the advice of you here we stopped the meets between Scooby and Willow as he had made her scream (although he didn't injure or bite her) he just growled and acted a bit aggressive. The biggest problem we have got is that because Scooby has the run of our house we don't have anywhere neutral, even the garden we just let him free roam and I am really cautious about putting them both into a place that I cant immediately access!! A couple of things weve noticed..... Scooby started chewing the rug by our door in summer as he knew that was the way in and out (way before she arrived) to stop him accessing the rug we placed a large fabric dog carrier in front of the door which we filled with hay, his very own hay house when he wanted to chill out. He has never ever weed or pooped anywhere except his litter tray in his cage. Since we got willow he has pooped all around her cage and weed and pooped in his hay house! I had to clean it all out and cause its fabric and I don't want him to wee on the fabric I placed a litter tray in there, I figured if he was going to toilet in there I would prefer it in a tray. Both rabbits have time out and during this time out both rabbits have used the tray. Scooby is no longer scrabbling at her through the bars and he is no longer growling through bars, he also remains calm when she is out whereby he used to go nuts!!. I lifted her out of her cage this morning and was knelt by the cage and he was having head rubs. He sniffed her and I kept on rubbing his head and then he did growl a bit but because I felt vulnerable I popped her back before anything could happen. I don't really know if im going in the right direction or not??????

I thought you were going to wait a while to give her chance to mature? I was just reading the last thread of yours where you say he growls and gets a bit aggressive if you have the female on your knee. This is because he is the dominant rabbit and should get the attention instead of her. Also apparently, large breeds mature more slowly than normal sized rabbits so something else to take into consideration.

Yes we are going to wait, today wasn't a planned meet I was just feeding her and he approached as she climbed onto my knee. I just wanted to know that the smelly poo will at some point stop and reassurance that its a good sign that he no longer really takes as much notice of her?