If we are taking a promissory note as collateral what is the correct way to perfect it under article 9? Does it matter whether it is secured by a deed of trust and if so what is the difference?

Perfection is possession as long as that note receivable is endorsed to your financial institution. You need to determine if the assignment should be with or without recourse to the assignee. You also want to record as assignment of that underlying deed of trust, assigning it to your financial institution.