stbx and i are seperated for 1 year i left the family home that we own together and moved in with friends now am setteled and would like to have joint custody we have not filed for div yet but will soon question is who decides custody am asking for cutody 40 per if she declines who decides a judge any help will be appreciated

It depends on what state you are in and the local county. For ex: state law does not require mediation where I am at...However the judge will not decide until the parties try to reach a settlement and go through Mediation with a Mediator and then go to court.
So yes the ultimate decision is made by a judge if the two parties can not agree.