We use Sage for Invoicing and Payroll and, as the two link together, it is pretty easy to do - the only more difficult time is year end when it is probably best to get your accountant to at least check what you are doing before you submit.
IMO paying an accountant for 2 employees, however litle he may charge, is totally unnecessary with the availaiblity of cost effective sopftware applications which can do it for you.
The other piece of advices I would give are pasword protect your application and take lots of regular backups (i.e. every time you do something in the application ideally) and store them safely off site - the great thing about regular backups especially with a small number of employees is if you do make a screw up you can easily restore to the last backup and start again.