Linked accounts double count entries

As an example, my cash management account and my linked mortgage account both show the payment as a negative, so it gets double counted.
Is the solution not to have the mortgage account download the transactions? Or will that stop it from automatically updating the principle owed?
On a side note, it would also be nice if there was a way to automate splitting the mortgage payment into principle, interest, insurance escrow, and tax escrow.

The double counting also occurs with the property management distributions being counted twice.