Yes it will show you the total of both. If you are looking at a summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 form and make sure it's right. Check lines 4b & 5b for any taxable amounts. For a rollover line b should be zero and the word Rollover by it.
They should be on separate lines on your 1040. The 401k rollover to IRA should be on line 5a with 0 on 5b saying Rollover.
The IRA to ROTH IRA is a conversion and the taxable amount should be on 1040 line 4b. Make sure you check the little IRA box between boxes 7&8 on the 1099R.
