The airlines are pretty firm about the fact that points go into the employee's accounts and not the employer's. They have obvious business reasons for wanting to do this. (First, it causes individual employees to favor their airline even when it's not cheapest; second individual employees are less likely to redeem the points at all or to redeem them optimally.)

Some carriers have programs oriented toward the company also; for example Delta has the "Skybonus" program.

How do you know your employees don't do anything with their miles?

And is it really worth it to you to book all these flights yourself (as you seem to do) rather than outsourcing to a travel agency? Well, that's your decision.