I think the issue is like this. That one employee whose salary at the time of joining was higher than Rs 15,000 was excluded from EPF. (You should have collected Form 11, which declared that he was NOT a member of EPF in his earlier establishments). Now he wants to get covered. You are also willing to contribute to PF.
If this is the situation, you should get a letter from the employee stating that he would like to be covered by PF and that he had earlier opted not to have PF, but from today's date, he would like to be part of it. Based on this request, you can cover him under PF. The date of his joining will be the current date and not his actual date of joining.
Again, since his salary is already above Rs 15,000, he should be covered only under EPF, and your (employer) contribution of 12% should be put under EPF alone without bifurcating it as 8.33% to the Pension Fund and 3.67% to PF.