The answer is less grammatical then colloquial, I think. "All employees" would normally be used to discuss employees as an abstract group—their needs and habits or what was required of them. "All the employees" would refer more specifically to a certain group of employees doing something in a particular moment. The second phrase is also a more casual form of the genitive "of the employees" whereas the first phrase is a nominative construction that talks about all employees as a single group; this is a further hint as to why the second tends to be more specific. I'm sure there are counter-examples, but this seems to be a good basic model:

"All employees are required to attend the mandatory training session."

"All employees receive a portion of their compensation as equity."

"It is important to think about the needs of all employees when making decisions about the future of a company."

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"All the employees were at the office Christmas party."

"All the employees sat in the break room."

"We talked to all (of) the employees present and quickly reached a decision."

<font color="#000000" face="Calibri" size="3">As I understand, the usage of an article in this case is according to the general rules of choosing articles. </font>

<font color="#000000" face="Calibri" size="3">E.g. “All employees have to read fire safety regulations”. </font>

<font color="#000000" face="Calibri" size="3">Here we talk about employees in general. We don’t mean a particular group. But we mean the whole staff of the company.</font>

<font color="#000000" face="Calibri" size="3">However, when we use “all the” we mean a particular group of people of a great many people. Like in your example: </font>"All the employees sat in the break room."

Here we mean the employees who came into the break room. Not the whole staff.