
Once you register with HMRC you will get a user number and have to select a password, I take it the free download is on the HMRC website. If this is the case you just need to log in from any PC/laptop with your details and be able to use it.
There should be no reason for the accountant to charge more as it is just a small exta step and the end of the payroll, should be gone in a flash for 2 employees but there are stories of companies having to fork out extra for this to external companies.