Each project that your office takes on should have its own unique project for Plant 3D. You'll want to organize all your project files into a unique network folder as well. Combining multiple office projects into one Plant 3D project would be risky in terms of potential data corruption. I have experienced entire projects becoming corrupt.
The way Plant 3D works best is by setting everything up at the beginning of the project (Iso and Ortho templates, project settings etc.). These settings could vary from project to project. Setting everything up correctly at the beginning is very important and will save you time and effort in the long run. Attributes like client name, project name etc can be controlled globally through the project setup to save time on title blocks.
All project related Autocad files should be controlled through the Project Manager. If you are planning on using Plant 3D for more than piping you should organize files in the Project Manager by discipline (Civil, Structural, Electrical, Piping etc.)
Piping models should be organized in a logical manner such as Unit>Area>Service>Line Number. Each "higher level" has a master model that references the lower level models. This makes the piping more manageable in terms of file size and when it comes time to make drawings. It also protects you in case of data corruption.
Piping file structure could be as follows
>Unit 1
>>Unit 1 Piping Master.dwg
>>Area 1
>>>Area 1 Piping Master.dwg
>>>>Area 1 Steam.dwg
>>>>>10-STEAM-CS300-0001.dwg
>>>>>10-STEAM-CS300-0002.dwg
>>>>Area 1 Service Water.dwg
>>>>>6-SW-CS150-0001.dwg
>>>>>8-SW-CS150-0001.dwg
>>>>Area 1 Slurry.dwg
>>>>>8-SLURRY-CS150-0001.dwg
These are just my opinions, you'll find what works best for your office and team through a little trial and error.
Let us know if you have further questions.