I am not sure if the company seal will work. In all eventuality, since the recommendation is a personal and not a professional intellectual piece of property, the manager or office personnel may not put a company seal. I think it has something to do with liability and professional practice. I found this out when my recommender told me that he would give his recos in plain paper and not on company letter head.
The other stratrgy you could follow is ask the administrative assistant to sign the letters. Just get an email from your manager letting the assistant know that it is ok and ask the assistant to type a letter for you and the school confirming the manager's approval.
This is your contingency option. If the company seal works, its great.