So did they even have a writing staff for those seasons, or was it all just him in an office somewhere by himself?
Pretty much. The only other writing staff that there'd been at all was Larry DiTillio, the story editor (who also wrote 7 episodes) for the first two seasons. Once it was cleared with the studio that JMS would be writing all of season 3, he was released.
The breakdown of JMS-written episodes was
S1 - 12
S2 - 15
S3 - 22
S4 - 22
S5 - 21