Just create a new account called 'Due To/From A' in Company B and 'Due To/From B' in company A. it can be set up as either an asset account or a liability account. At each of each month just compare the 2 accounts with each other to ensure they both reconcile to each other. When funds are transferred from A then A would record as a general journal entry CR Bank and DR Due to/From B, Then in B you would do the same journal entry to DR bank and CR Due to/from A.

In my case, the company owner often makes payments from her personal account and later (or before) writes cheques to herself to cover it.

I ended up setting up the "1065 [owner] for bill payment" account as an asset account like Smithco says.  (it can go contra (negative) from time to time - that doesn't matter).  The point of this post is that I set it up the "due" account as account class "bank", so I can make payments FROM it directly.

When she uses her personal interac to send cash to one of her contractors, I just enter a purchase by "cash" from "[owner] for bill payment" account.  No playing with the journal is needed.  

Then her cheques to herself are "other payment" from the regular chequing account for account 1065.

In my case, I'm only accounting for the entity on one side.  In your case, with both entities under your accounting, I think I agree with Smithco's "due to/from" terminology.