Sure, if you have both entities in the microflow, you can use a Change Object activity to set the value of an association on an entity, just like you can set the value of an attribute on an entity.
For instance, if you had Customer and Order entities with a 1 to M association between Customer and Order, and you had an instance of each one in a microflow, you could add a Change Object activity to the microflow, specify the Order entity to be changed and select the Customer---Order association as the item to be changed. Then specify $Customer as the value of that association.
I got it working. Thanks. I had to do two things. The associated entities are in two different modules and I had to define the association in the other module. And I had to define another microflow parameter for the outermost dataview entity. I am having trouble understanding what entities are in scope sometimes and bringing needed entities into scope in pages.