I am generating payslip report for the employees in Crystal Report tool (C# coding), based on from and to employee id's, the report gets generated.
I have to save the report in a PDF format based on employee wise (separate PDF document for every employees - split up), in a define path , by automatically (through programming), and also I have to encrypt the generated documents (password protected).
I will suggest a solution that is far from ideal, but since you are in a hurry, it may help.
To "separate pdf": generate one report for one employee at a time; or generate them all and use a tool to split the PDF.
About encryption, i don't know if the PDF format or the Adobe Reader has something ready to support it, but you could zip the files with password. I believe it can be done programatically or, at least, with batch commands.