It all depends on what you want to do.
In the past, we have typically gone in through provided API’s so we can take advantage of the business logic in the systems. If this is not something you need then you should be able to access the database directly.
I would build a single Orchestration for your process. If you need rollback if one call fails, it will be much more difficult.
You should be able to call the Java web service through Biztalk. Although, in the past I had to build a custom .net component to make the call since the input was an array of objects.
Hope this helps.