I have a single phase industrial control transformer 480 V/ 120 V, 1000 volt amps. Should I fuse the primary or the secondary?
Should both the primary and the secondary windings be fused, the maximum permissible fuse rating on the primary would be higher than that would be permissible, were the secondary not to be fused.
However, it is generally preferred to fuse both the primary and the secondary.
Recommended fuse ratings would be available in manufacturers' literature.
Since the 480 V primary winding would be across two phases, fuses would be required for each phase.
On the secondary side, with one end earthed, fuses would be required only at the other end.  It is standard practice to have multiple branches, with fuse ratings for each branch dependent on the cross-section of the cables used.