We have a pre-tax transportation program for commuting and parking costs. We use an outside vendor to reimburse employees by check when they submit a claim form. We pay an administrative fee to the vendor for each employee.

At one of our locations, the building offers parking to employees through the employer. The employer pays for the number of spots and then pays the building.
Rather than put these employees in our transit program through our vendor, can we just deduct the money pre-tax and pay the building directly for each employee's parking spot?

I would set it up as a separate 132(f) arrangement so that it qualifies under 132(f). There aren't significant document requirements, but I would want to have the basics in writing. (And there are no discrimination requirements, so you don't have to worry about who is in which arrangement.