You really can't use the same occupancy sensors for both security and automation with any kind of satisfactory result.
Security motion sensors are tuned to prevent false alarms so they don't nuisance trip, occupancy sensors for autoamtion on the other hand are tuned to trip at the slightest movement so the automation occurs reliably.
The two applications are polar opposites and really require different sensors.
Door and window contacts used for security can be used for automation with no problem.
As for lighting, you need to decide on a technology first.
Since you are posting this in the HAI section, I assume you have an Omni panel.
There are several options available depending on your budget and the level of DIY you are willing to undertake.
Many DIY people, like me, chose the UPB (HLC) power line carrier (PLC) lighting technology.
I chose it for it's relatively low cost, expandability, availaility of units and DIY friendly programming.
The Omni panel also comes with a UPB interface by default.
There is also Z-wave and to a lesser extent Zigbee and ALC in addition to some of the higher end technologies like Centralite.
X-10 is also an option, but that is really a dinosaur relative to the current technologies.
Since you are at the "clean slate" stage, it is probably helpful to read about the different technologies to decide which one best fits your needs.
There is a great UPB primer in the resource section.