Company X:

Easiest is to set up a 'wages payable' liability account and tag it as a 'bank' in Sage.  Then, each paycheque that was paid with the other company's chequebook can be 'paid' using the 'wages payable' account, by switching the bank at the top right of the screen.

This will create liabilities in the 'wages payable' account, which can then be cleared by general journal entry, probably debit 'wages payable' and credit 'owed to Company Y'.

Company Y:

Here, the transactions would likely just be debit 'Due from Company X' and credit bank.

Company X:

Easiest is to set up a 'wages payable' liability account and tag it as a 'bank' in Sage.  Then, each paycheque that was paid with the other company's chequebook can be 'paid' using the 'wages payable' account, by switching the bank at the top right of the screen.

This will create liabilities in the 'wages payable' account, which can then be cleared by general journal entry, probably debit 'wages payable' and credit 'owed to Company Y'.

Company Y:

Here, the transactions would likely just be debit 'Due from Company X' and credit bank.