I am not sure I understand your issue correctly. But looks like the issue is the basic dashboard size.
If you have multiple dashboards within a workbook, when published all the dashboards will come up with the size of the largest dashboard.
I haven't found a workaround for this. You may need to use empty containers to fill in the extra space or plan to have both the dashboards in the same size.
You are right all the dashboards will come up with the size of the largest dashboard. In my case Dashboard B is largest, and I have a sheet at the bottom of the Dashboard B. This Dashboard B's sheet link(using action filter) to Dashboard A's sheet, located on top portion of dashboard A. When I click the Dashboard B's bottom sheet, it goes to black bottom portion of dashboard A. Does it make more sense?
Can you share a sample workbook.