I've formatted your queries, and it looks like you were very close... you just didn't have the ON condition for your join
gmdc_employee AS a
JOIN gmdc_user AS b
on a.employee_id = b.employee_id
( a.employee_name like'%$search%'
OR b.employee_name like '%$search%' )
AND b.company_name like 'DLSU'
I'm not really sure this is the proper join is by the employee ID or not... you don't show any instances of same "employee" vs "user". With no "ON" condition, its basically going to create a Cartesian join otherwise (or outright error out)... You may also want to logically OR if you are looking for multiple criteria... such as the name found in one field OR the other... if found in both, no problem...