Retirement tax questions

I tried entering the one 1099-R form twice to portray the $40,000 rollover transaction as a two-step process (even though it wasn't) and that only increases my income total by an additional $40,000.  The receiving institution (Vanguard) didn't think I needed a 1099-R from them since I didn't actually do the conversion in two-steps with them but just did the direct one-step rollover.  This is why I'm having such trouble!