Here are some articles to get you started with the how to.

[1]  https://accountants.intuit.com/support/en-us/help-search?document_type=Articles&filter=ProConnect%20...

Done correctly the credits should be generated automatically. 

[2]Be clear about residency.  Is there a permanent home in which they would "normally" live together. That should likely be the resident state.  Otherwise your scenario looks reasonable, assuming each state allows that. 

[3] Yes, three credits will be charged. What about MFJ VA with a bunch of part year resdiences? 

Definitely a time eater and very much NOT my favorite client. They are likely talking to you because the previous preparer charged too much. Let they know you will charge more and hopefully they go away (unless you are enjoying this intrusion into your valuable time.)