Missed itr for last year

You must immediately print out a copy of your ITR from income tax website, sign it and send it by post to Bangalore. If you don't do it, it means your ITR filing is pending/incomplete, and you may face penalty for it. Online submission is complete only if you digitally sign the xml file. If xml file is not digitally signed, than you have to post the "signed" printout physically to Bangalore and get a stamped copy back from Bangalore as authentication of receipt of your income tax return by income tax office.

For AY 2011-12, you must consult an income tax specialist. While income under the head salary will be clubbed for both Form -16, income from other heads like HP, Other Sources should not be clubbed. Further ensure that deductions under Chapter VIA have not been taken twice.

Further, in instances like yours, it often happens that you end up taking benefit of Section 80C and basic exemption limit twice in each Form 16, so you end up paying less tax. Since, July 31, being last date for AY 2011-12 has already passed, you must immediately file your return for AY 2011-12 else you will incur heavy interest on tax liability due. 

Regards,

Jagrut