Joe, this is possible. When you add a rule to a decision diamond, it will say, “If the [Contact’s]” then the next option that shows up brings up a list of all custom field categories you can select from. Once you select a category, you can then select the actual custom field and its value.
I will also add that for customers who have multiple of your branches selected and you only want them in one sequence, you will have to add rules to the diamond (by selecting “+AND”) for each sequence that say the value for the other 5 branches doesn’t equal yes, or whatever you have it set to.
Does this help?