Even if your business is only paying one Director, you will probably hear from the pensions regulator as they will ask you to confirm you are compliant.
Not all employees are subject to the auto enrolement rules, but all employers need to be aware of their responsibilities as they can change with the age of your employees, the salaries paid to your employees and even how many staff you have on the books.
There is a lot of information out there about pensions and what the thresholds and the rules are. If you are registering a PAYE scheme it would definitley be worth reading up about the rules so that you can get the right systems put in place at the right times.
The sums can probably be taken care of by your software provider, but it is definitely worth making sure that the software can synch to the pension provider you choose, as it is more straightforward than having to log the deductions manually each month. Ask your software provider before you sign up.