You're doing fine, I think what your missing is an Entity Relationship Diagram.
Once you have that your Dataflow will make more sense.
Then you need to link your data flows to the ERD.
Fancy tools won't help, you'll just spend more time fighting with the tools than understanding the problem.
Data Flows alone work if the data is fairly simple, but otherwise you need to start with your ERD first.
I think it's fine to use Visio for the overview and Word and Excel for the nitty gritty.
Once you have that your Dataflow will make more sense.
Then you need to link your data flows to the ERD.
Fancy tools won't help, you'll just spend more time fighting with the tools than understanding the problem.
Data Flows alone work if the data is fairly simple, but otherwise you need to start with your ERD first.
I think it's fine to use Visio for the overview and Word and Excel for the nitty gritty.
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