If a couple is separating and they live on post, is the spouse entitled to 80% of the BAH?

Read through AR 608-99, paragraph 2-6. It's not 80%. It will depend on a number of factors, including the presence (or absence) of a court order or agreement, the total number of supported family members, any family member(s) from previous marriages, whether or not she is staying in housing, etc.

That is a question that is not easy to answer. Go to JAG and they will lay it all out for you.

SGT (Anonymous): Inform your soldier to immediately get to a family law attorney who specializes in military issues in family law. This soldier needs to understand every aspect of the divorce/separation under both the military law and the civilian law of the state where he is currently located. To ignore this is at the service member's peril as the spouse may be able to get back payments for spousal maintenance, child support, etc.
AR608-99 becomes effective the date of the separation if there is no oral/written agreement or court order. Oral agreements will remain effective until one side disagrees that there is an oral agreement; at that point, AR608-99 becomes effective. So until the wife moves out, there is no requirement to pay any support to the wife as she is living in government housing. Once she moves out, then the service member is required to pay the entire BAH with dependent rate to her. Furthermore, there are then the pro rata shares which will need to be determined if the service member has a child support order from a previous relation. All of this gets rather complicated. And if the service member is paying for anything related to the actual house/apartment where the wife moves to during the separation, that can be considered family support.
The service member needs to get a legal separation agreement put in place as soon as possible so as to ensure that debts are allocated to each person, assets are properly divided, and any spousal maintenance is set. The legal separation agreement can be later turned into a Divorce Decree should the couple end up divorcing. It's a good protection for the service member and I have had several cases where I have drafted these agreements. In some cases the couples reconciled. More often though, they ended up getting divorced. If the service member knows reconciliation is not on the list, then he needs to file for the divorce and obtain temporary court orders regarding spousal maintenance. The legal separation agreement or temporary court order will effectively nullify AR608-99 as it sets forth what is considered to be support. Hence, get your service member to a civilian family law attorney ASAP.