How to visually configure dependency between data

I need to set the relationship between two sets of data. The sets can be big, with hundreds of records. After some research, I found that some applications use a dependency matrix, like in this example from Salesforce:

The idea is to set the relationship between a "Controlling set" and a "Dependent set".

But it is difficult to visualize large sets of data, as the amount of columns grow and you need to paginate horizontally.

So, I'm thinking about using this model instead:

The idea is having two lists, a selecting one for the controlling set and the other one for the dependent set (one to many relationship).

I also could have many to many relationships. Where a dependent record could be associated with one, two or more controlling records. In this case I would be able to also select from dependent set to controlling set, like in this image:

Do you think this is an easier, more usable way to solve the problem? Or do you have any other suggestions?

Thank you!