If I understand you correctly the main problem is the location of the sub-diagram in your model overview?
This is by design; a sub diagram isn’t linked to another diagram but to one of its model elements instead. That’s why it’ll be placed ‘underneath’ the model element in the project browser.
If you want to reference another diagram but without moving its physical location then consider using the reference option. If you click on a model element then you’ll find the indicator in the lower left corner (instead of the lower right corner which is used for sub diagrams). There you can select an existing diagram. You can also add references in the specification screen (press enter when you have a model element selected).
This will add an indicator in the lower left corner, and if you click that you can switch to another diagram just as before. The main difference is that your diagram(s) won’t change their location.
Referencing can be especially useful if you need to refer to diagrams which are located in another model structure (analysis vs. design for example).