My son and daughters biological father tried to kill me and my husband and went to prision for 8-15 yrs. My son was 2yrs and my daughter was just a baby. They call me husband dad and he want's to adopted. The biological father just took me to court to have contact with then and a judge denied him any contact with them. So how does my husband go about adopting them

Legally he can not adopt if the bio father does not consent.
I think your best bet would be to request the same Judge for your options because he already seems to be on your side.