If the account that you put your shared rent payments into was only used for the purpose of paying rent, and you have proof of those transactions, and of the paying of rent, this should be sufficient in the case of an audit.
You could use a monthly reimbursement check (or electronic bank transfer) from one company to another and split it as negative expenses (rebate) per category. For example,
Deposit Withdrawal Account Memo
$100 Internet For A and B
$500 Rent For A and B
$100 Gas/Electric For A ...