Inter company transactions are best handled via the Transfer of funds through a DUE TO / DUE FROM Account. 

Some businesses have two accounts. For a given Company A, the first account - DUE TO B - is a liability account that represents the money Company A owes to Company B.  The second account - DUE FROM B - is an asset account that represents the money Company B owes to Company A.

Some businesses have one account.  Company A would create a liability account DUE TO / DUE FROM B to represent both things.  A positive balance means Company B owes Company A money.  A negative balance means Company B owes Company A money.

This example will use a single account.

1. Setup a Journal in each Company. 

Switch Companies to the Parent:

The Parent Journal is named "Subsidiary" to indicate the flow of funds to and from the subsidiary:

Create the “Bank” Account 112500 P during the creation of the Journal:

… so you can use it on the Payments Configuration tab:

Switch Companies to the Subsidiary:

The Subsidiary Journal is named "Parent" to indicate the flow of funds to and from the Parent:

Be sure to create the "Bank" Account during setup, like with the first Journal, and select that same account on the Payments Configuration tab, like with the first Journal.

2. For each funding transaction, transfer funds in both Companies, using the Internal Transfer feature of each Journal:

Switch Companies to the Parent:

Send money to the Subsidiary:

First, use the Parent Bank Journal:

This is the first step of the Internal Transfer, removing the money from the Bank Account.

Next, use the Subsidiary Journal:

This is the second step of the Internal Transfer, recording the amount owed from the Subsidiary.

After completing both steps, you have now credited your Parent Bank account and debited the Due To / Due From account to indicate that the Subsidiary owes you $10,000.

Parent Company Journal Entries after both steps are complete:

Note: Until Bank reconcilation is complete, the bank credit stays in the Outstanding Payments account.

First, use the Subsidiary Bank Journal:

This is the first step of the Internal Transfer, receive the money into the Bank Account.

Next, use the Parent Journal:

This is the second step of the Internal Transfer, recording the amount owed to the Parent.

After completing both steps, you have now debited your Subsidiary Bank account and credited the Due To / Due From account to indicate that you owe the Parent $10,000.

Subsidiary Company Journal Entries after both steps are complete:

The partial Parent Balance Sheet after funding:

All Journal Entries: