Using the actual expense method, can I apply the business use percentage to tolls?

You can't estimate the amounts paid in tolls based on business mileage relative to total mileage.  You must use the act tolls paid when the vehicle was used for business.

Tolls incurred for business  are not subject to  limitations ... you will add the full amount of tolls paid in addition to any other vehicle expenses you take. So enter only the tolls incurred for business.