In 2010 I rolled over all of my stocks (no cash) from my SEP-IRA to my qualified Roth, and chose to pay the taxes in 2011 and 2012. While preparing my 2012 return, I note that, apparently though some oversight of my own, I did not re-enter the numbers onto lines 25a and 25b (they were entered onto 20a and 20b). I am actually thinking of going ahead and paying all of the taxes this year, but if I don't, how would I amend 2010 to reflect my intentions. It only makes a difference of about $600 in taxes due, plus penalty, I am sure.

It sounds like you're using a 1040A, a/k/a the bane of my existence, but here's what should be on your 2010 and 2011 returns on the IRA distribution line (line 15 of the civilized 1040, line "n" here):

2010: line n(a): the amount of the conversion, as reflected on the 1099-R. Line n(b): zero. On Form 8606 the box electing to have the conversion taxed in 2010 is not checked.

2011: line n(a): zero. Line n(b): 50% of the conversion amount. No 8606 is required.

Phil
Rule Your Retirement Home Fool