To go to Nara by train, depart from Kyoto Station or Tofukuji Station. JR Nara line.
Both stations are located about 12-15 min walk from your stay but different direction.
Tofukuji station is nearer to Nara but only one station from Kyoto station.
If you want to stop and check some shops in Kyoto station or nearby, it’ll be nice to start from Kyoto station.
If you want to see local atmosphere, it’ll be interesting starting from Tofukuji station.
Here is train planning website, just for your information: