The 3/5 Compromise actually came up for debate during the formation of the Articles of Confederation. Under the Articles of Confederation, direct taxes were calculated according to land value in each state. To cut down on the amount of tax each state would have to pay, the values of the land were undervalued. To fix this, the proposal was for direct taxes to be calculated according to population. Thus came into question about the slaves in the South. Would the slaves be counted or not counted when figuring out taxes? The Father of the Constitution, James Madison, came up with the number 3/5. Now, Rhode Island (go figure) and New Hampshire did not vote for the compromise. Under the Articles of Confederation, each state has 1 vote and voting had to be unanimous. The 3/5 Compromise failed.
Over a decade later, after the failure of the Articles, a new form of government was being created. During the Constitutional Convention in 1787, the 3/5 Compromise was brought back up for discussion and debate. This time, the emphasis on the Compromise was not taxes, but representation in Congress, specifically the House of Representatives. The number of delegates from each state in the House is based on population. It was not James Madison, but James Wilson of Pennsylvania, that proposed the Compromise to gain favor with the southern states. Over the long term, the Compromise was not very affective. The northern states began to grow faster than the southern states, yet the Compromise managed to help elect slave-holding Presidents from 1800-1850.
source of information: http://www.digitalhistory.uh.edu/documents/documents_p2.cfm?doc=306