Q:

Can a Jew own a business that employs or pays atheist Jews on Shabbat? 

I am an atheist who happens to be Jewish, and would like to work for a business owned by a religious Jew. 

Is he allowed to pay me for my work on Shabbat? 
What if the payment is global (e.g. 10% of a full time job), and not for specific hours, but the owner knows that most likely, a lot of the work will be done on Shabbat? 
If I were a gentile, would he have an easier time paying me for work on Shabbat? 

A:

The difficulty you are experiencing comes about because according to the religious viewpoint, one who does not observe the commandments is a sinning Jew, but still a Jew.  The Sages stated, "A Jew, even if he sins, is a Jew" Sanhedrin 44a. 
As Rabbi Yaakov Menken expresses it: 

A person who is born into the Jewish people, even a sincere convert
  who later turns away from Judaism, remains a Jew.  Even if he sins, he
  remains one of the Children of Israel. 

You sincerely feel that you are an atheist; according to the religious viewpoint, you remain a Jew. 
The result is that your employer cannot enable you to work on Shabbat, still less pay you for that.  
You ask “If I were a gentile, would he have an easier time paying me for work on Shabbat?”  The employer might find some permission to employ a gentile on Shabbat.  But in line with the discussion above, you cannot become a gentile. 