Did some get a bonus 2 years? Did some get a shorter 4 year term? It seems the Founders wanted Senatorial elections staggered. After the first few cycles it is clear how it works. But how was the original 2 year staggering established?
The first US Senate comprised of 20 Senators (from 10 states - North Carolina and Rhode Island didn't ratify the Constitution until after the First Senate gathered to meet, and the New York legislature hadn't picked its Senators yet).
A special committee divided the Senate into three "classes", making sure that each class was balanced geographically, and that only one Senator per state was in a class.
On May 15, 1789, three Senators from each class were assigned to pick classes by lottery, meaning a representative from each group was asked to literally pick a piece of paper with a number on it from a box with Vice President John Adams and 12 of the 20 Senators in attendance. Tristram Dalton of Massachusetts went first, and picked "Class One". He and six other Senators were Class One, and would serve two years (ie, their terms expired in 1791). It's not clear how the rest of the slips were chosen, but seven Senators ended up getting the "Class Two" slot and served for four years, while six were "Class Three" serving for the full six years.
Source: US Senate Historical Office