@CWM59
Yes, it is best to have Co. B reimburse Co. A because you want to have all of this off of Co. A's books and you want to properly record the EMD paid in Co. B so you can transfer that to the property asset account when you close.
To do this, in Co. A, set up an other current asset account called 'Due from Co. B'. In Co. B, set up an other current liability account called 'Due to Co. A'. Also, if you haven't already, set up Co. A as a vendor in Co. B and set up Co. B as a customer in Co. A.
Then,
1) In Co. A, assign the EMD check to the newly-created 'Due from Co. B' asset account.
2) In Co. B, create a journal entry, debit the account you use for EMDs, credit the newly-created 'Due to Co. A' liability account.
3) In Co. B, write the reimbursement check and assign it to the 'Due to Co. A' liability account.
4) In Co. A, deposit the check and assign it to the newly-created 'Due from Co. B' asset account.
Now, you have everything off of Co. A's books and you have the EMD ready to be applied at closing.
