just copy the numbers exactly how they are on the piece of paper into Turbo tax. Many of the field will be blank and that is okay.
$xxxx.xx from line 1 will end up on line 4a of Form 1040 - this reflects the rollover only - no tax impact
$0.00 from line 2a will end up on line 4b of Form 1040 - this reflects what is taxable, but obviously nothing is.
there is not going to be an impact on the tax refund (or the taxes owed) because line 2a of the 109-R form is zero.
I am not really following all the movement you are describing between companies A and B, but if you actually received the cash from the 401(k) and kept it, I suspect there is another Form 1099-R that will arrive shortly from Company A (the form you have received is from Company B, right?). These firms are supposed to send 1099-R's by January 31st.