You can have several project files (.ppj) in same folder and in PellesC 8 project sources must be in same or folders below that folder.
Use project workspace to keep together those project files.
For example:
hello_workspace includes hello.ppj and hello64.ppj and common source for project is hello.c or src/hello.c
Problems is that target exe/dll/lib name and output folder must be different, if you don't want to build whole 32/64 project every time.