Using different bank account for Invoicing clients

Your basic premise has problems.  each business is required to have its' own set of accounts and transactions, in QBO that would mean two subscriptions

That said, the invoice has nothing to do with where the money received is deposited.  The invoice, well actually the item on the invoice posts income, then you deposit that income to the bank account of your choice

This is one legal entity which has 2 business units.  Aware that the income/expense can be segregated using the class function - which we are currently using.  But would like to know if multiple bank accounts can be selected at the time of billing customers.

Thanks for your prompt reply, @savita-clearnexu.

Selecting multiple bank accounts when billing your customers isn't available. Also, you can only select one bank account when receiving invoice payments. 

As a way around, you'll want to create a separate invoice for each business unit. This way, you'll be able to deposit the payments to your preferred bank account. I'll show you how.

1. Create an invoice for Unit 1 in your QuickBooks Online (QBO).
2. Once your customer pays for it, record the payment and deposit it to your Bank account 1.
3. Do the same process for your Unit 2.

I'd also recommend working with your accountant for additional guidance. They can advise you on other ways to record this and ensure the accuracy of your accounts. 

Once you're all set, you might want to utilize this link for guidance in efficiently matching your bank and QuickBooks balance: Reconcile an account in QuickBooks Online.

You can always count on me if you need more help with your invoices and bank deposits. Just add the details in your reply and I'll get back to you as soon as possible. Keep safe, and have a great weekend ahead!