* Finally, understand your firm's responsibilities should a loss occur. Regulation E, which is part of the Electronic Fund Transfer Act, provides protection to individual consumers engaging in electronic fund transfers. "It doesn't extend to commercial accounts," says Austin. Instead, the extent of your firm's liability, as well as your bank's, should be covered in the contract between the two organizations, says Doug Johnson, vice president for risk management policy with the American Bankers Association.

What's more, even if the bank takes on some responsibility to cover a loss, it may hinge on your company instituting reasonable security procedures. "By contract, the business generally agrees to abide by reasonable security procedures," Johnson says. If your company experiences a loss and it becomes apparent that its security policies were sub-par, the bank may not be liable for any losses.