How do you deal with filing various fed/state taxes?

Ever since we have hired employee, its getting painful to track all the various taxes to Fed, IRS, State government, even a small startup needs to keep track and file. Quickbook seems to do some job, but it do not provides notifications for very many things. I wonder how other folks are handling this? Do they have smart CPAs and bookkeeper who actively monitor and manage this? Or are there other softwares available?