EPF - pay the EPF separately for each site through a different challan for each site?

I have a private security agency. I have more than one principal employers and more than one site. One, can I pay the EPF separately for each site through a different challan for each site. Two, what do I enter in the column where it says total numbers of employees and number of employees left out.

Its always better to Pay PF only one code & at one location only to track record of all employee at a Go.

query itself is incomplete, has many sites means several meaning, such as many principals or many code numbers or many states .....please put specific clear query