If a check is made out to an employee for services, is our company okay to deposit the check and then pay the employee via check or payroll?

The only reasons for you to handle this check would be 

1. what the employee is to receive is less than the check amount
2. it is company income

Two choices if this is company income erroneously made out to employee.

1. employee cashes check and brings amount to you

2. employee endorses check over to company and you deposit

What you do with these funds after you receive them is up to you and what they were for.  An employee sales commission should go through the books as it is considered W2 wages