It can be one of three ways:
1) John, Sr, John Jr., John III, John IV, etc. (normally the first person doesn't need to add Sr. to his name because his birth certificate doesn't say Sr. But, the next generation's birth certificate must say JR. or II. )
2) Just plain John, (or John, I) John II, John III, John IV, etc.
3) Here's another way:
Father is William Jones; Son is William Jones, Jr. Then he has another son and he names him after his own father: Such as: Thomas Jones and he would be Thomas Jones II.
For the sake of the families probably they all have nick-names to tell them apart. LOL
Is this more confusing to you? I hope not!