I would be direct and rational and tell his father how it is. I would say something to the effect of "I realize you came from a different generation but it's 2016 and your comments are racist and unacceptable in my home. You can say what you wish in your own home but I will not tollerate it here. Please use the bathroom in the bedroom if you can help it. I find myself cleaning urine from the floor in the bathroom you are using and either I have a UTI and am leaking, or someone is peeing on the floor without realizing it. Let's avoid blame by having you stick to the bathroom we got ready for you. Please do not go through my things. It makes me uncomfortable"

If he ignores you, don't allow him to stay. If he's racist in his own home, don't go there. If your BF is racist and it's unacceptable to you, you would be smart to leave.