I happen to start a new ROTH IRA account in April 2010 after filing my 2009 returns. As this was before tax filing tax deadline, I contributed towards 2009, I also contributed towards 2010 ROTH IRA in Feb 2011. Previously I have also been contributing a traditional IRA via savings account since last 4-5 years. While filing my taxes this year I found that I exceeded my overall contribution limits for IRAs in both 2009 and 2010. (When I opened the ROTH account I was not aware that IRA limits are applicable to traditional and ROTH combined) I removed the excess contribution of 2010 with almost nil earnings in March 2011, however my 2009 ROTH has ripped some gains($1200-1300). I have also removed excess contribution for 2009 as well. I assume I will be required to pay 6% excise for my excess contribution of 2009. I wanted to know what are my options.
1] Am i required to file 2009 amended return now?
2] what about earnings? Do i need to pay 10% penalty for withdrawals in addition to 6% excise on earnings?
3] can I pay for excise as part of 2010 return or wait until I receive 1099-R from my ROTH custodian? (I assume i will not receive that until Jan-2012)

Will appreciate some kind guidance.

Thank you in advance.