I am about to appear for IIT-JEE 2014.Since IIT-JEE shall then be ISEET... how much does going to college matter?.... and what boards should I join(CBSE, ICSE or STATE)?

It does not take to the boards for appering JEE. For changed pattern of JEE you must be well prepared from the bginning to the end. Whatever your intrest take that board and study perfectly. As Board marks are also under consideration you should consider the board where you feel no stress and be happy to prepare.