I love my lion head to death but they can be an onry breed! Mine girl is territorial and doesn't like being handled. They are known to be independent as they get older (Lilo is almost 2). But she's sweet if you let her come to you and she rarely bites (just nips). We had some difficulty bonding...
The first time I had to give Lilo medicine she peed on my pillow afterwards so I know what you mean about him being mad at you lol what my vet said is to mash up a banana and mix the medicine in with it then spoon feed it to them. It.worked great with Lilo because she LOVES bananas.
Honestly its up to the rabbit. My lion head does all her business in the litter box but my Dutch won't even go near it. Rabbits poop where they want. If she's pooping.in.a different corner maybe try 2 boxes?