Last year in June, my residency status for tax purposes got converted to 'resident alien' as I started my degree in Sept 2004 and completed 5 calendar years in US as a student in 2009. Hence the IRS website (pub 519) says that I need to file form 1040. However, since I was on fellowship through out the year I received only form 1042S from my univ (no W2), that too indicating my taxable income as that received before June 2009. My first question is what to do with the income I received after June. Secondly, In form 1040 they only mention about W2 and there is no mention of how to file using 1042S. I was wondering should I just use the corresponding columns in 1042S to complete 1040 or is there any other form for this situation. Also if I use 1040 should I include income in line 7 or 21.

I even tried to use efile turbotax free version suggested on IRS website, but it did not give option for 1042S. Then I tried to file considering my income as received from scholarships but there were no subsequent sections in which it asked for federal tax withheld. Hence, it later indicated that I need to pay underpayment penalty as it assumed that no income was withheld which was not the case.

Provide info -- what is in each box of 1042-S.