If you're not comfortable with what the accountant is doing, go to a different tax professional. (Not all accountants are tax experts.) Bring copies of your original tax return, the first amended return, your W-2, and any 1099-R forms or other tax forms that you received.
I'm not sure we can help you here. There is a lot of information missing, and we can't see your tax returns. But here are some questions that might help to clarify the situation.
"This is the 2nd amendment to correct the 1st amendment that I'm pretty sure was not done correctly."
Why did you file the first amended return? What was wrong with the original tax return?
Has the IRS completed processing of the first amended return, and sent you a notice that it was complete?
"I rolled over almost 80k"
Rolled over from what to what? From a 401(k) plan to a traditional IRA, or some other types of accounts? How many 1099-R forms did you receive, and from which accounts? On each 1099-R, what are the amounts in boxes 1 and 2a, and what is the distribution code in box 7? Is the IRA/SEP/SIMPLE box checked?
"it is showing the 80k + 40k"
"with it showing 120k"
What is "it" that shows $120K? The original tax return, the first amended return, the second amended return, or something else? What form and line number shows $120K?
"he showed me the form preview where only the taxable amount is 40k."
What form and line number?
"It is also showing 40k in 4a and 4b and I researched that 4a should be blank."
Again, what is "it"? (I assume it's a Form 1040, but is it the original one that you filed, or a revised Form 1040 that reflects one or both of the amendments?) You are only giving rounded or approximate numbers. Are the amounts on Form 1040 lines 4a and 4b exactly the same? What are the exact amounts? They should not be the same, but I don't think that that in itself is a serious problem. If lines 4a and 4b are not exactly the same, ask the accountant to explain the difference.
