I am sure you know that Autopatcher is a 3rd party package that includes latest security updates whereas SP3 is developed by MS. For better support and seamless integration, go for SP3 only. I suppose you can use Autopatcher on sp3 too in order to install more recent security updates.
Autopatcher allows you to add the updates to your system, but it is not for service packs. Also, SP3 is a collection of updates for your system, but there are many newer updates to be added after SP3 was released.
So, you first need to install SP3 on your system. Then, you can use Autopatcher or the built in Windows Update to download and install the newer updates.