Either input should work. If you cannot get sufficient levels running line in with the input gain cranked up, switch to microphone in which is a more sensitive input. If you can get good levels through either, try it both ways and see if both recordings sound similar or if one has less noise during quiet parts.
The main features the DR2d has which other handhelds don't is the DUAL recording function. If you don't use that than either recorder should do the job. The DR2d also has an IR remote control if that's important to you.