I don't think you need to worry about entering the $2 underestimated tax payment anywhere on the amended California return. If that's what you did initially, and the reject followed, it's probably the cause of the reject.
The reject code wouldn't seem to explain actually what's causing the problem, based on what you're saying.
But, what appears to be hanging you up with the amended return is the Box 8 Penalties/Interest amount on Schedule X. There's no box on the amended return for underpayment of estimated tax. And, if you'll look at the instructions for Schedule X, there's very vague guidance for penalties and interest, but nothing about underpayment of estimated tax.
On the other hand, if you'll look at the original return, Form 540, Line 112 is used for Interest, late return penalties, and late payment penalties, and there's a separate Line 113 for Underpayment of estimated tax. The Instructions for Form 540 reflect this, as well.
So, entering your underpayment into the penalty field would be like trying to put a square peg into a round hole, and apparently California's efile program recognizes it.
That said… if you can't remove the $2 at this point and your amended return continues to reject, you'll just need to go ahead and paper-file.
