If you have this relationship:
Company::Company_UUID = Branch::Company_ID
then you should have all that you need for your conditional value list.
Are you familiar with these links on conditional value lists?
Forum Tutorial: Custom Value List?
Knowledgebase article: http://help.filemaker.com/app/answers/detail/a_id/5833/kw/conditional%20value%20list
Hierarchical Conditional Value lists: Conditional Value List Question
Feel free to post follow up questions here if those links aren't enough to get your value lists working correctly.